ERX538157 E-MTAB-2805:G1_cell8 E-MTAB-2805:G1_cell8 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527258 SAMEA2699524 E-MTAB-2805:G1_cell8 G1_cell8 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538158 E-MTAB-2805:S_cell69 E-MTAB-2805:S_cell69 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527259 SAMEA2699525 E-MTAB-2805:S_cell69 S_cell69 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538159 E-MTAB-2805:G1_cell23 E-MTAB-2805:G1_cell23 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527260 SAMEA2699526 E-MTAB-2805:G1_cell23 G1_cell23 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538160 E-MTAB-2805:G1_cell94 E-MTAB-2805:G1_cell94 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527261 SAMEA2699527 E-MTAB-2805:G1_cell94 G1_cell94 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538161 E-MTAB-2805:G1_cell45 E-MTAB-2805:G1_cell45 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527262 SAMEA2699528 E-MTAB-2805:G1_cell45 G1_cell45 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538213 E-MTAB-2805:S_cell57 E-MTAB-2805:S_cell57 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527314 SAMEA2699580 E-MTAB-2805:S_cell57 S_cell57 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538214 E-MTAB-2805:G2M_cell2 E-MTAB-2805:G2M_cell2 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527315 SAMEA2699581 E-MTAB-2805:G2M_cell2 G2M_cell2 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538215 E-MTAB-2805:S_cell48 E-MTAB-2805:S_cell48 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527316 SAMEA2699582 E-MTAB-2805:S_cell48 S_cell48 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538216 E-MTAB-2805:G1_cell15 E-MTAB-2805:G1_cell15 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527317 SAMEA2699583 E-MTAB-2805:G1_cell15 G1_cell15 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538217 E-MTAB-2805:S_cell84 E-MTAB-2805:S_cell84 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527318 SAMEA2699584 E-MTAB-2805:S_cell84 S_cell84 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538293 E-MTAB-2805:G1_cell82 E-MTAB-2805:G1_cell82 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527394 SAMEA2699660 E-MTAB-2805:G1_cell82 G1_cell82 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538294 E-MTAB-2805:S_cell41 E-MTAB-2805:S_cell41 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527395 SAMEA2699661 E-MTAB-2805:S_cell41 S_cell41 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538295 E-MTAB-2805:G2M_cell42 E-MTAB-2805:G2M_cell42 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527396 SAMEA2699662 E-MTAB-2805:G2M_cell42 G2M_cell42 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538296 E-MTAB-2805:G2M_cell59 E-MTAB-2805:G2M_cell59 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527397 SAMEA2699663 E-MTAB-2805:G2M_cell59 G2M_cell59 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538297 E-MTAB-2805:G2M_cell36 E-MTAB-2805:G2M_cell36 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527398 SAMEA2699664 E-MTAB-2805:G2M_cell36 G2M_cell36 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538373 E-MTAB-2805:G1_cell7 E-MTAB-2805:G1_cell7 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527474 SAMEA2699740 E-MTAB-2805:G1_cell7 G1_cell7 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538374 E-MTAB-2805:S_cell43 E-MTAB-2805:S_cell43 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527475 SAMEA2699741 E-MTAB-2805:S_cell43 S_cell43 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538375 E-MTAB-2805:G1_cell51 E-MTAB-2805:G1_cell51 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527476 SAMEA2699742 E-MTAB-2805:G1_cell51 G1_cell51 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538376 E-MTAB-2805:S_cell83 E-MTAB-2805:S_cell83 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527477 SAMEA2699743 E-MTAB-2805:S_cell83 S_cell83 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538377 E-MTAB-2805:S_cell70 E-MTAB-2805:S_cell70 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527478 SAMEA2699744 E-MTAB-2805:S_cell70 S_cell70 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538218 E-MTAB-2805:G1_cell89 E-MTAB-2805:G1_cell89 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527319 SAMEA2699585 E-MTAB-2805:G1_cell89 G1_cell89 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538219 E-MTAB-2805:G2M_cell61 E-MTAB-2805:G2M_cell61 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527320 SAMEA2699586 E-MTAB-2805:G2M_cell61 G2M_cell61 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538220 E-MTAB-2805:G1_cell43 E-MTAB-2805:G1_cell43 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527321 SAMEA2699587 E-MTAB-2805:G1_cell43 G1_cell43 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538221 E-MTAB-2805:G2M_cell3 E-MTAB-2805:G2M_cell3 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527322 SAMEA2699588 E-MTAB-2805:G2M_cell3 G2M_cell3 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538222 E-MTAB-2805:S_cell12 E-MTAB-2805:S_cell12 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527323 SAMEA2699589 E-MTAB-2805:S_cell12 S_cell12 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538298 E-MTAB-2805:G1_cell92 E-MTAB-2805:G1_cell92 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527399 SAMEA2699665 E-MTAB-2805:G1_cell92 G1_cell92 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538299 E-MTAB-2805:G2M_cell28 E-MTAB-2805:G2M_cell28 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527400 SAMEA2699666 E-MTAB-2805:G2M_cell28 G2M_cell28 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538300 E-MTAB-2805:G1_cell74 E-MTAB-2805:G1_cell74 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527401 SAMEA2699667 E-MTAB-2805:G1_cell74 G1_cell74 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538301 E-MTAB-2805:G1_cell42 E-MTAB-2805:G1_cell42 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527402 SAMEA2699668 E-MTAB-2805:G1_cell42 G1_cell42 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538302 E-MTAB-2805:S_cell15 E-MTAB-2805:S_cell15 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527403 SAMEA2699669 E-MTAB-2805:S_cell15 S_cell15 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538378 E-MTAB-2805:G2M_cell94 E-MTAB-2805:G2M_cell94 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527479 SAMEA2699745 E-MTAB-2805:G2M_cell94 G2M_cell94 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538379 E-MTAB-2805:G1_cell83 E-MTAB-2805:G1_cell83 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527480 SAMEA2699746 E-MTAB-2805:G1_cell83 G1_cell83 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538380 E-MTAB-2805:G2M_cell29 E-MTAB-2805:G2M_cell29 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527481 SAMEA2699747 E-MTAB-2805:G2M_cell29 G2M_cell29 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538381 E-MTAB-2805:S_cell31 E-MTAB-2805:S_cell31 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527482 SAMEA2699748 E-MTAB-2805:S_cell31 S_cell31 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538382 E-MTAB-2805:G2M_cell16 E-MTAB-2805:G2M_cell16 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527483 SAMEA2699749 E-MTAB-2805:G2M_cell16 G2M_cell16 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538223 E-MTAB-2805:G1_cell44 E-MTAB-2805:G1_cell44 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527324 SAMEA2699590 E-MTAB-2805:G1_cell44 G1_cell44 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538224 E-MTAB-2805:G2M_cell20 E-MTAB-2805:G2M_cell20 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527325 SAMEA2699591 E-MTAB-2805:G2M_cell20 G2M_cell20 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538225 E-MTAB-2805:G1_cell93 E-MTAB-2805:G1_cell93 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527326 SAMEA2699592 E-MTAB-2805:G1_cell93 G1_cell93 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538226 E-MTAB-2805:G1_cell30 E-MTAB-2805:G1_cell30 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527327 SAMEA2699593 E-MTAB-2805:G1_cell30 G1_cell30 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538227 E-MTAB-2805:G2M_cell27 E-MTAB-2805:G2M_cell27 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527328 SAMEA2699594 E-MTAB-2805:G2M_cell27 G2M_cell27 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538303 E-MTAB-2805:G1_cell57 E-MTAB-2805:G1_cell57 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527404 SAMEA2699670 E-MTAB-2805:G1_cell57 G1_cell57 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538304 E-MTAB-2805:G1_cell39 E-MTAB-2805:G1_cell39 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527405 SAMEA2699671 E-MTAB-2805:G1_cell39 G1_cell39 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538305 E-MTAB-2805:G2M_cell24 E-MTAB-2805:G2M_cell24 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527406 SAMEA2699672 E-MTAB-2805:G2M_cell24 G2M_cell24 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538306 E-MTAB-2805:G1_cell87 E-MTAB-2805:G1_cell87 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527407 SAMEA2699673 E-MTAB-2805:G1_cell87 G1_cell87 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538307 E-MTAB-2805:S_cell7 E-MTAB-2805:S_cell7 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527408 SAMEA2699674 E-MTAB-2805:S_cell7 S_cell7 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538383 E-MTAB-2805:S_cell34 E-MTAB-2805:S_cell34 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527484 SAMEA2699750 E-MTAB-2805:S_cell34 S_cell34 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538384 E-MTAB-2805:G1_cell96 E-MTAB-2805:G1_cell96 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527485 SAMEA2699751 E-MTAB-2805:G1_cell96 G1_cell96 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538385 E-MTAB-2805:G2M_cell9 E-MTAB-2805:G2M_cell9 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527486 SAMEA2699752 E-MTAB-2805:G2M_cell9 G2M_cell9 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538386 E-MTAB-2805:G2M_cell52 E-MTAB-2805:G2M_cell52 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527487 SAMEA2699753 E-MTAB-2805:G2M_cell52 G2M_cell52 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538387 E-MTAB-2805:G1_cell35 E-MTAB-2805:G1_cell35 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527488 SAMEA2699754 E-MTAB-2805:G1_cell35 G1_cell35 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538228 E-MTAB-2805:G1_cell53 E-MTAB-2805:G1_cell53 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527329 SAMEA2699595 E-MTAB-2805:G1_cell53 G1_cell53 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538229 E-MTAB-2805:S_cell14 E-MTAB-2805:S_cell14 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527330 SAMEA2699596 E-MTAB-2805:S_cell14 S_cell14 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538230 E-MTAB-2805:G1_cell22 E-MTAB-2805:G1_cell22 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527331 SAMEA2699597 E-MTAB-2805:G1_cell22 G1_cell22 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538231 E-MTAB-2805:S_cell73 E-MTAB-2805:S_cell73 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527332 SAMEA2699598 E-MTAB-2805:S_cell73 S_cell73 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538232 E-MTAB-2805:S_cell1 E-MTAB-2805:S_cell1 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527333 SAMEA2699599 E-MTAB-2805:S_cell1 S_cell1 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538308 E-MTAB-2805:G2M_cell84 E-MTAB-2805:G2M_cell84 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527409 SAMEA2699675 E-MTAB-2805:G2M_cell84 G2M_cell84 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538309 E-MTAB-2805:G2M_cell60 E-MTAB-2805:G2M_cell60 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527410 SAMEA2699676 E-MTAB-2805:G2M_cell60 G2M_cell60 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538310 E-MTAB-2805:G1_cell79 E-MTAB-2805:G1_cell79 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527411 SAMEA2699677 E-MTAB-2805:G1_cell79 G1_cell79 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538311 E-MTAB-2805:S_cell35 E-MTAB-2805:S_cell35 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527412 SAMEA2699678 E-MTAB-2805:S_cell35 S_cell35 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538312 E-MTAB-2805:G1_cell78 E-MTAB-2805:G1_cell78 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527413 SAMEA2699679 E-MTAB-2805:G1_cell78 G1_cell78 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538388 E-MTAB-2805:G1_cell56 E-MTAB-2805:G1_cell56 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527489 SAMEA2699755 E-MTAB-2805:G1_cell56 G1_cell56 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538389 E-MTAB-2805:G2M_cell74 E-MTAB-2805:G2M_cell74 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527490 SAMEA2699756 E-MTAB-2805:G2M_cell74 G2M_cell74 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538390 E-MTAB-2805:G1_cell21 E-MTAB-2805:G1_cell21 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527491 SAMEA2699757 E-MTAB-2805:G1_cell21 G1_cell21 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538391 E-MTAB-2805:G1_cell73 E-MTAB-2805:G1_cell73 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527492 SAMEA2699758 E-MTAB-2805:G1_cell73 G1_cell73 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538392 E-MTAB-2805:S_cell75 E-MTAB-2805:S_cell75 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527493 SAMEA2699759 E-MTAB-2805:S_cell75 S_cell75 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538233 E-MTAB-2805:G2M_cell50 E-MTAB-2805:G2M_cell50 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527334 SAMEA2699600 E-MTAB-2805:G2M_cell50 G2M_cell50 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538234 E-MTAB-2805:S_cell28 E-MTAB-2805:S_cell28 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527335 SAMEA2699601 E-MTAB-2805:S_cell28 S_cell28 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538235 E-MTAB-2805:G2M_cell57 E-MTAB-2805:G2M_cell57 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527336 SAMEA2699602 E-MTAB-2805:G2M_cell57 G2M_cell57 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538236 E-MTAB-2805:G2M_cell92 E-MTAB-2805:G2M_cell92 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527337 SAMEA2699603 E-MTAB-2805:G2M_cell92 G2M_cell92 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538237 E-MTAB-2805:S_cell30 E-MTAB-2805:S_cell30 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527338 SAMEA2699604 E-MTAB-2805:S_cell30 S_cell30 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538313 E-MTAB-2805:G1_cell34 E-MTAB-2805:G1_cell34 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527414 SAMEA2699680 E-MTAB-2805:G1_cell34 G1_cell34 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538314 E-MTAB-2805:S_cell91 E-MTAB-2805:S_cell91 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527415 SAMEA2699681 E-MTAB-2805:S_cell91 S_cell91 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538315 E-MTAB-2805:G2M_cell47 E-MTAB-2805:G2M_cell47 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527416 SAMEA2699682 E-MTAB-2805:G2M_cell47 G2M_cell47 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538316 E-MTAB-2805:S_cell25 E-MTAB-2805:S_cell25 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527417 SAMEA2699683 E-MTAB-2805:S_cell25 S_cell25 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538317 E-MTAB-2805:S_cell3 E-MTAB-2805:S_cell3 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527418 SAMEA2699684 E-MTAB-2805:S_cell3 S_cell3 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538393 E-MTAB-2805:G2M_cell41 E-MTAB-2805:G2M_cell41 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527494 SAMEA2699760 E-MTAB-2805:G2M_cell41 G2M_cell41 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538394 E-MTAB-2805:G1_cell31 E-MTAB-2805:G1_cell31 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527495 SAMEA2699761 E-MTAB-2805:G1_cell31 G1_cell31 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538395 E-MTAB-2805:G2M_cell63 E-MTAB-2805:G2M_cell63 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527496 SAMEA2699762 E-MTAB-2805:G2M_cell63 G2M_cell63 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538396 E-MTAB-2805:S_cell63 E-MTAB-2805:S_cell63 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527497 SAMEA2699763 E-MTAB-2805:S_cell63 S_cell63 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538397 E-MTAB-2805:G1_cell58 E-MTAB-2805:G1_cell58 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527498 SAMEA2699764 E-MTAB-2805:G1_cell58 G1_cell58 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538162 E-MTAB-2805:S_cell47 E-MTAB-2805:S_cell47 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527263 SAMEA2699529 E-MTAB-2805:S_cell47 S_cell47 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538238 E-MTAB-2805:G1_cell86 E-MTAB-2805:G1_cell86 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527339 SAMEA2699605 E-MTAB-2805:G1_cell86 G1_cell86 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538239 E-MTAB-2805:G1_cell72 E-MTAB-2805:G1_cell72 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527340 SAMEA2699606 E-MTAB-2805:G1_cell72 G1_cell72 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538240 E-MTAB-2805:G1_cell29 E-MTAB-2805:G1_cell29 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527341 SAMEA2699607 E-MTAB-2805:G1_cell29 G1_cell29 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538241 E-MTAB-2805:G1_cell18 E-MTAB-2805:G1_cell18 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527342 SAMEA2699608 E-MTAB-2805:G1_cell18 G1_cell18 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538242 E-MTAB-2805:S_cell42 E-MTAB-2805:S_cell42 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527343 SAMEA2699609 E-MTAB-2805:S_cell42 S_cell42 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538318 E-MTAB-2805:G2M_cell19 E-MTAB-2805:G2M_cell19 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527419 SAMEA2699685 E-MTAB-2805:G2M_cell19 G2M_cell19 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538319 E-MTAB-2805:G1_cell65 E-MTAB-2805:G1_cell65 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527420 SAMEA2699686 E-MTAB-2805:G1_cell65 G1_cell65 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538320 E-MTAB-2805:G2M_cell71 E-MTAB-2805:G2M_cell71 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527421 SAMEA2699687 E-MTAB-2805:G2M_cell71 G2M_cell71 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538321 E-MTAB-2805:S_cell29 E-MTAB-2805:S_cell29 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527422 SAMEA2699688 E-MTAB-2805:S_cell29 S_cell29 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538322 E-MTAB-2805:S_cell82 E-MTAB-2805:S_cell82 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527423 SAMEA2699689 E-MTAB-2805:S_cell82 S_cell82 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538398 E-MTAB-2805:G2M_cell49 E-MTAB-2805:G2M_cell49 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527499 SAMEA2699765 E-MTAB-2805:G2M_cell49 G2M_cell49 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538399 E-MTAB-2805:S_cell19 E-MTAB-2805:S_cell19 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527500 SAMEA2699766 E-MTAB-2805:S_cell19 S_cell19 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538400 E-MTAB-2805:S_cell92 E-MTAB-2805:S_cell92 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527501 SAMEA2699767 E-MTAB-2805:S_cell92 S_cell92 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538401 E-MTAB-2805:G2M_cell90 E-MTAB-2805:G2M_cell90 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527502 SAMEA2699768 E-MTAB-2805:G2M_cell90 G2M_cell90 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538402 E-MTAB-2805:G2M_cell39 E-MTAB-2805:G2M_cell39 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527503 SAMEA2699769 E-MTAB-2805:G2M_cell39 G2M_cell39 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538163 E-MTAB-2805:G2M_cell93 E-MTAB-2805:G2M_cell93 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527264 SAMEA2699530 E-MTAB-2805:G2M_cell93 G2M_cell93 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538164 E-MTAB-2805:G1_cell77 E-MTAB-2805:G1_cell77 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527265 SAMEA2699531 E-MTAB-2805:G1_cell77 G1_cell77 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538165 E-MTAB-2805:G2M_cell73 E-MTAB-2805:G2M_cell73 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527266 SAMEA2699532 E-MTAB-2805:G2M_cell73 G2M_cell73 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538166 E-MTAB-2805:G2M_cell8 E-MTAB-2805:G2M_cell8 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527267 SAMEA2699533 E-MTAB-2805:G2M_cell8 G2M_cell8 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538167 E-MTAB-2805:G1_cell17 E-MTAB-2805:G1_cell17 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527268 SAMEA2699534 E-MTAB-2805:G1_cell17 G1_cell17 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538243 E-MTAB-2805:G1_cell38 E-MTAB-2805:G1_cell38 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527344 SAMEA2699610 E-MTAB-2805:G1_cell38 G1_cell38 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538244 E-MTAB-2805:S_cell88 E-MTAB-2805:S_cell88 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527345 SAMEA2699611 E-MTAB-2805:S_cell88 S_cell88 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538245 E-MTAB-2805:G2M_cell32 E-MTAB-2805:G2M_cell32 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527346 SAMEA2699612 E-MTAB-2805:G2M_cell32 G2M_cell32 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538246 E-MTAB-2805:G1_cell64 E-MTAB-2805:G1_cell64 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527347 SAMEA2699613 E-MTAB-2805:G1_cell64 G1_cell64 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538247 E-MTAB-2805:S_cell9 E-MTAB-2805:S_cell9 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527348 SAMEA2699614 E-MTAB-2805:S_cell9 S_cell9 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538323 E-MTAB-2805:G2M_cell67 E-MTAB-2805:G2M_cell67 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527424 SAMEA2699690 E-MTAB-2805:G2M_cell67 G2M_cell67 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538324 E-MTAB-2805:G2M_cell55 E-MTAB-2805:G2M_cell55 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527425 SAMEA2699691 E-MTAB-2805:G2M_cell55 G2M_cell55 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538325 E-MTAB-2805:S_cell10 E-MTAB-2805:S_cell10 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527426 SAMEA2699692 E-MTAB-2805:S_cell10 S_cell10 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538326 E-MTAB-2805:G2M_cell77 E-MTAB-2805:G2M_cell77 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527427 SAMEA2699693 E-MTAB-2805:G2M_cell77 G2M_cell77 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538327 E-MTAB-2805:G2M_cell45 E-MTAB-2805:G2M_cell45 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527428 SAMEA2699694 E-MTAB-2805:G2M_cell45 G2M_cell45 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538403 E-MTAB-2805:G1_cell46 E-MTAB-2805:G1_cell46 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527504 SAMEA2699770 E-MTAB-2805:G1_cell46 G1_cell46 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538404 E-MTAB-2805:G1_cell16 E-MTAB-2805:G1_cell16 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527505 SAMEA2699771 E-MTAB-2805:G1_cell16 G1_cell16 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538405 E-MTAB-2805:S_cell95 E-MTAB-2805:S_cell95 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527506 SAMEA2699772 E-MTAB-2805:S_cell95 S_cell95 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538406 E-MTAB-2805:G2M_cell70 E-MTAB-2805:G2M_cell70 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527507 SAMEA2699773 E-MTAB-2805:G2M_cell70 G2M_cell70 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538407 E-MTAB-2805:S_cell24 E-MTAB-2805:S_cell24 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527508 SAMEA2699774 E-MTAB-2805:S_cell24 S_cell24 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538168 E-MTAB-2805:S_cell18 E-MTAB-2805:S_cell18 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527269 SAMEA2699535 E-MTAB-2805:S_cell18 S_cell18 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538169 E-MTAB-2805:G2M_cell40 E-MTAB-2805:G2M_cell40 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527270 SAMEA2699536 E-MTAB-2805:G2M_cell40 G2M_cell40 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538170 E-MTAB-2805:S_cell71 E-MTAB-2805:S_cell71 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527271 SAMEA2699537 E-MTAB-2805:S_cell71 S_cell71 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538171 E-MTAB-2805:G1_cell85 E-MTAB-2805:G1_cell85 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527272 SAMEA2699538 E-MTAB-2805:G1_cell85 G1_cell85 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538172 E-MTAB-2805:G2M_cell65 E-MTAB-2805:G2M_cell65 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527273 SAMEA2699539 E-MTAB-2805:G2M_cell65 G2M_cell65 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538248 E-MTAB-2805:G2M_cell46 E-MTAB-2805:G2M_cell46 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527349 SAMEA2699615 E-MTAB-2805:G2M_cell46 G2M_cell46 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538249 E-MTAB-2805:G1_cell11 E-MTAB-2805:G1_cell11 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527350 SAMEA2699616 E-MTAB-2805:G1_cell11 G1_cell11 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538250 E-MTAB-2805:G2M_cell7 E-MTAB-2805:G2M_cell7 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527351 SAMEA2699617 E-MTAB-2805:G2M_cell7 G2M_cell7 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538251 E-MTAB-2805:G2M_cell37 E-MTAB-2805:G2M_cell37 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527352 SAMEA2699618 E-MTAB-2805:G2M_cell37 G2M_cell37 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538252 E-MTAB-2805:S_cell2 E-MTAB-2805:S_cell2 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527353 SAMEA2699619 E-MTAB-2805:S_cell2 S_cell2 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538328 E-MTAB-2805:S_cell21 E-MTAB-2805:S_cell21 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527429 SAMEA2699695 E-MTAB-2805:S_cell21 S_cell21 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538329 E-MTAB-2805:S_cell62 E-MTAB-2805:S_cell62 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527430 SAMEA2699696 E-MTAB-2805:S_cell62 S_cell62 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538330 E-MTAB-2805:G2M_cell95 E-MTAB-2805:G2M_cell95 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527431 SAMEA2699697 E-MTAB-2805:G2M_cell95 G2M_cell95 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538331 E-MTAB-2805:G1_cell5 E-MTAB-2805:G1_cell5 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527432 SAMEA2699698 E-MTAB-2805:G1_cell5 G1_cell5 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538332 E-MTAB-2805:G1_cell81 E-MTAB-2805:G1_cell81 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527433 SAMEA2699699 E-MTAB-2805:G1_cell81 G1_cell81 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538408 E-MTAB-2805:G2M_cell96 E-MTAB-2805:G2M_cell96 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527509 SAMEA2699775 E-MTAB-2805:G2M_cell96 G2M_cell96 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538409 E-MTAB-2805:S_cell67 E-MTAB-2805:S_cell67 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527510 SAMEA2699776 E-MTAB-2805:S_cell67 S_cell67 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538410 E-MTAB-2805:S_cell51 E-MTAB-2805:S_cell51 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527511 SAMEA2699777 E-MTAB-2805:S_cell51 S_cell51 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538411 E-MTAB-2805:G1_cell91 E-MTAB-2805:G1_cell91 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527512 SAMEA2699778 E-MTAB-2805:G1_cell91 G1_cell91 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538412 E-MTAB-2805:S_cell61 E-MTAB-2805:S_cell61 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527513 SAMEA2699779 E-MTAB-2805:S_cell61 S_cell61 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538173 E-MTAB-2805:G2M_cell38 E-MTAB-2805:G2M_cell38 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527274 SAMEA2699540 E-MTAB-2805:G2M_cell38 G2M_cell38 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538174 E-MTAB-2805:G2M_cell13 E-MTAB-2805:G2M_cell13 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527275 SAMEA2699541 E-MTAB-2805:G2M_cell13 G2M_cell13 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538175 E-MTAB-2805:G1_cell55 E-MTAB-2805:G1_cell55 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527276 SAMEA2699542 E-MTAB-2805:G1_cell55 G1_cell55 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538176 E-MTAB-2805:S_cell58 E-MTAB-2805:S_cell58 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527277 SAMEA2699543 E-MTAB-2805:S_cell58 S_cell58 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538177 E-MTAB-2805:S_cell86 E-MTAB-2805:S_cell86 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527278 SAMEA2699544 E-MTAB-2805:S_cell86 S_cell86 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538253 E-MTAB-2805:G1_cell71 E-MTAB-2805:G1_cell71 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527354 SAMEA2699620 E-MTAB-2805:G1_cell71 G1_cell71 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538254 E-MTAB-2805:G1_cell19 E-MTAB-2805:G1_cell19 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527355 SAMEA2699621 E-MTAB-2805:G1_cell19 G1_cell19 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538255 E-MTAB-2805:G2M_cell72 E-MTAB-2805:G2M_cell72 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527356 SAMEA2699622 E-MTAB-2805:G2M_cell72 G2M_cell72 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538256 E-MTAB-2805:G1_cell6 E-MTAB-2805:G1_cell6 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527357 SAMEA2699623 E-MTAB-2805:G1_cell6 G1_cell6 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538257 E-MTAB-2805:S_cell54 E-MTAB-2805:S_cell54 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527358 SAMEA2699624 E-MTAB-2805:S_cell54 S_cell54 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538333 E-MTAB-2805:G1_cell25 E-MTAB-2805:G1_cell25 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527434 SAMEA2699700 E-MTAB-2805:G1_cell25 G1_cell25 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538334 E-MTAB-2805:G1_cell12 E-MTAB-2805:G1_cell12 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527435 SAMEA2699701 E-MTAB-2805:G1_cell12 G1_cell12 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538335 E-MTAB-2805:G2M_cell68 E-MTAB-2805:G2M_cell68 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527436 SAMEA2699702 E-MTAB-2805:G2M_cell68 G2M_cell68 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538336 E-MTAB-2805:G2M_cell23 E-MTAB-2805:G2M_cell23 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527437 SAMEA2699703 E-MTAB-2805:G2M_cell23 G2M_cell23 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538337 E-MTAB-2805:G2M_cell10 E-MTAB-2805:G2M_cell10 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527438 SAMEA2699704 E-MTAB-2805:G2M_cell10 G2M_cell10 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538413 E-MTAB-2805:S_cell77 E-MTAB-2805:S_cell77 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527514 SAMEA2699780 E-MTAB-2805:S_cell77 S_cell77 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538414 E-MTAB-2805:G2M_cell5 E-MTAB-2805:G2M_cell5 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527515 SAMEA2699781 E-MTAB-2805:G2M_cell5 G2M_cell5 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538415 E-MTAB-2805:S_cell33 E-MTAB-2805:S_cell33 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527516 SAMEA2699782 E-MTAB-2805:S_cell33 S_cell33 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538416 E-MTAB-2805:S_cell17 E-MTAB-2805:S_cell17 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527517 SAMEA2699783 E-MTAB-2805:S_cell17 S_cell17 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538417 E-MTAB-2805:G2M_cell79 E-MTAB-2805:G2M_cell79 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527518 SAMEA2699784 E-MTAB-2805:G2M_cell79 G2M_cell79 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538178 E-MTAB-2805:G2M_cell58 E-MTAB-2805:G2M_cell58 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527279 SAMEA2699545 E-MTAB-2805:G2M_cell58 G2M_cell58 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538179 E-MTAB-2805:G2M_cell82 E-MTAB-2805:G2M_cell82 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527280 SAMEA2699546 E-MTAB-2805:G2M_cell82 G2M_cell82 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538180 E-MTAB-2805:G2M_cell53 E-MTAB-2805:G2M_cell53 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527281 SAMEA2699547 E-MTAB-2805:G2M_cell53 G2M_cell53 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538181 E-MTAB-2805:G1_cell2 E-MTAB-2805:G1_cell2 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527282 SAMEA2699548 E-MTAB-2805:G1_cell2 G1_cell2 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538182 E-MTAB-2805:G1_cell27 E-MTAB-2805:G1_cell27 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527283 SAMEA2699549 E-MTAB-2805:G1_cell27 G1_cell27 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538258 E-MTAB-2805:G1_cell10 E-MTAB-2805:G1_cell10 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527359 SAMEA2699625 E-MTAB-2805:G1_cell10 G1_cell10 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538259 E-MTAB-2805:G2M_cell11 E-MTAB-2805:G2M_cell11 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527360 SAMEA2699626 E-MTAB-2805:G2M_cell11 G2M_cell11 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538260 E-MTAB-2805:G2M_cell81 E-MTAB-2805:G2M_cell81 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527361 SAMEA2699627 E-MTAB-2805:G2M_cell81 G2M_cell81 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538261 E-MTAB-2805:S_cell87 E-MTAB-2805:S_cell87 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527362 SAMEA2699628 E-MTAB-2805:S_cell87 S_cell87 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538262 E-MTAB-2805:G1_cell41 E-MTAB-2805:G1_cell41 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527363 SAMEA2699629 E-MTAB-2805:G1_cell41 G1_cell41 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538338 E-MTAB-2805:S_cell45 E-MTAB-2805:S_cell45 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527439 SAMEA2699705 E-MTAB-2805:S_cell45 S_cell45 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538339 E-MTAB-2805:G1_cell4 E-MTAB-2805:G1_cell4 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527440 SAMEA2699706 E-MTAB-2805:G1_cell4 G1_cell4 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538340 E-MTAB-2805:G2M_cell6 E-MTAB-2805:G2M_cell6 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527441 SAMEA2699707 E-MTAB-2805:G2M_cell6 G2M_cell6 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538341 E-MTAB-2805:G1_cell20 E-MTAB-2805:G1_cell20 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527442 SAMEA2699708 E-MTAB-2805:G1_cell20 G1_cell20 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538342 E-MTAB-2805:S_cell8 E-MTAB-2805:S_cell8 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527443 SAMEA2699709 E-MTAB-2805:S_cell8 S_cell8 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538418 E-MTAB-2805:G1_cell84 E-MTAB-2805:G1_cell84 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527519 SAMEA2699785 E-MTAB-2805:G1_cell84 G1_cell84 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538419 E-MTAB-2805:G2M_cell78 E-MTAB-2805:G2M_cell78 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527520 SAMEA2699786 E-MTAB-2805:G2M_cell78 G2M_cell78 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538420 E-MTAB-2805:G1_cell62 E-MTAB-2805:G1_cell62 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527521 SAMEA2699787 E-MTAB-2805:G1_cell62 G1_cell62 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538421 E-MTAB-2805:G2M_cell34 E-MTAB-2805:G2M_cell34 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527522 SAMEA2699788 E-MTAB-2805:G2M_cell34 G2M_cell34 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538422 E-MTAB-2805:G1_cell3 E-MTAB-2805:G1_cell3 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527523 SAMEA2699789 E-MTAB-2805:G1_cell3 G1_cell3 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538183 E-MTAB-2805:G2M_cell48 E-MTAB-2805:G2M_cell48 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527284 SAMEA2699550 E-MTAB-2805:G2M_cell48 G2M_cell48 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538184 E-MTAB-2805:S_cell38 E-MTAB-2805:S_cell38 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527285 SAMEA2699551 E-MTAB-2805:S_cell38 S_cell38 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538185 E-MTAB-2805:S_cell74 E-MTAB-2805:S_cell74 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527286 SAMEA2699552 E-MTAB-2805:S_cell74 S_cell74 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538186 E-MTAB-2805:G1_cell54 E-MTAB-2805:G1_cell54 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527287 SAMEA2699553 E-MTAB-2805:G1_cell54 G1_cell54 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538187 E-MTAB-2805:G1_cell49 E-MTAB-2805:G1_cell49 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527288 SAMEA2699554 E-MTAB-2805:G1_cell49 G1_cell49 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538263 E-MTAB-2805:S_cell44 E-MTAB-2805:S_cell44 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527364 SAMEA2699630 E-MTAB-2805:S_cell44 S_cell44 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538264 E-MTAB-2805:G1_cell60 E-MTAB-2805:G1_cell60 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527365 SAMEA2699631 E-MTAB-2805:G1_cell60 G1_cell60 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538265 E-MTAB-2805:G1_cell48 E-MTAB-2805:G1_cell48 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527366 SAMEA2699632 E-MTAB-2805:G1_cell48 G1_cell48 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538266 E-MTAB-2805:G2M_cell69 E-MTAB-2805:G2M_cell69 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527367 SAMEA2699633 E-MTAB-2805:G2M_cell69 G2M_cell69 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538267 E-MTAB-2805:S_cell39 E-MTAB-2805:S_cell39 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527368 SAMEA2699634 E-MTAB-2805:S_cell39 S_cell39 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538343 E-MTAB-2805:S_cell76 E-MTAB-2805:S_cell76 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527444 SAMEA2699710 E-MTAB-2805:S_cell76 S_cell76 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538344 E-MTAB-2805:G2M_cell30 E-MTAB-2805:G2M_cell30 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527445 SAMEA2699711 E-MTAB-2805:G2M_cell30 G2M_cell30 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538345 E-MTAB-2805:S_cell40 E-MTAB-2805:S_cell40 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527446 SAMEA2699712 E-MTAB-2805:S_cell40 S_cell40 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538346 E-MTAB-2805:G1_cell36 E-MTAB-2805:G1_cell36 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527447 SAMEA2699713 E-MTAB-2805:G1_cell36 G1_cell36 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538347 E-MTAB-2805:G1_cell90 E-MTAB-2805:G1_cell90 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527448 SAMEA2699714 E-MTAB-2805:G1_cell90 G1_cell90 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538135 E-MTAB-2805:S_cell80 E-MTAB-2805:S_cell80 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527236 SAMEA2699502 E-MTAB-2805:S_cell80 S_cell80 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538136 E-MTAB-2805:G2M_cell1 E-MTAB-2805:G2M_cell1 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527237 SAMEA2699503 E-MTAB-2805:G2M_cell1 G2M_cell1 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538188 E-MTAB-2805:G2M_cell33 E-MTAB-2805:G2M_cell33 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527289 SAMEA2699555 E-MTAB-2805:G2M_cell33 G2M_cell33 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538189 E-MTAB-2805:G2M_cell88 E-MTAB-2805:G2M_cell88 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527290 SAMEA2699556 E-MTAB-2805:G2M_cell88 G2M_cell88 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538190 E-MTAB-2805:G2M_cell62 E-MTAB-2805:G2M_cell62 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527291 SAMEA2699557 E-MTAB-2805:G2M_cell62 G2M_cell62 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538191 E-MTAB-2805:G2M_cell22 E-MTAB-2805:G2M_cell22 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527292 SAMEA2699558 E-MTAB-2805:G2M_cell22 G2M_cell22 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538192 E-MTAB-2805:G1_cell50 E-MTAB-2805:G1_cell50 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527293 SAMEA2699559 E-MTAB-2805:G1_cell50 G1_cell50 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538268 E-MTAB-2805:S_cell36 E-MTAB-2805:S_cell36 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527369 SAMEA2699635 E-MTAB-2805:S_cell36 S_cell36 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538269 E-MTAB-2805:G2M_cell18 E-MTAB-2805:G2M_cell18 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527370 SAMEA2699636 E-MTAB-2805:G2M_cell18 G2M_cell18 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538270 E-MTAB-2805:S_cell79 E-MTAB-2805:S_cell79 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527371 SAMEA2699637 E-MTAB-2805:S_cell79 S_cell79 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538271 E-MTAB-2805:G2M_cell87 E-MTAB-2805:G2M_cell87 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527372 SAMEA2699638 E-MTAB-2805:G2M_cell87 G2M_cell87 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538272 E-MTAB-2805:G2M_cell83 E-MTAB-2805:G2M_cell83 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527373 SAMEA2699639 E-MTAB-2805:G2M_cell83 G2M_cell83 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538348 E-MTAB-2805:G2M_cell85 E-MTAB-2805:G2M_cell85 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527449 SAMEA2699715 E-MTAB-2805:G2M_cell85 G2M_cell85 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538349 E-MTAB-2805:G1_cell69 E-MTAB-2805:G1_cell69 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527450 SAMEA2699716 E-MTAB-2805:G1_cell69 G1_cell69 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538350 E-MTAB-2805:G2M_cell14 E-MTAB-2805:G2M_cell14 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527451 SAMEA2699717 E-MTAB-2805:G2M_cell14 G2M_cell14 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538351 E-MTAB-2805:S_cell26 E-MTAB-2805:S_cell26 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527452 SAMEA2699718 E-MTAB-2805:S_cell26 S_cell26 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538352 E-MTAB-2805:S_cell16 E-MTAB-2805:S_cell16 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527453 SAMEA2699719 E-MTAB-2805:S_cell16 S_cell16 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538137 E-MTAB-2805:S_cell65 E-MTAB-2805:S_cell65 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527238 SAMEA2699504 E-MTAB-2805:S_cell65 S_cell65 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538138 E-MTAB-2805:S_cell89 E-MTAB-2805:S_cell89 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527239 SAMEA2699505 E-MTAB-2805:S_cell89 S_cell89 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538139 E-MTAB-2805:G2M_cell66 E-MTAB-2805:G2M_cell66 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527240 SAMEA2699506 E-MTAB-2805:G2M_cell66 G2M_cell66 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538140 E-MTAB-2805:G1_cell14 E-MTAB-2805:G1_cell14 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527241 SAMEA2699507 E-MTAB-2805:G1_cell14 G1_cell14 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538141 E-MTAB-2805:G1_cell40 E-MTAB-2805:G1_cell40 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527242 SAMEA2699508 E-MTAB-2805:G1_cell40 G1_cell40 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538193 E-MTAB-2805:G1_cell63 E-MTAB-2805:G1_cell63 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527294 SAMEA2699560 E-MTAB-2805:G1_cell63 G1_cell63 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538194 E-MTAB-2805:G1_cell61 E-MTAB-2805:G1_cell61 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527295 SAMEA2699561 E-MTAB-2805:G1_cell61 G1_cell61 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538195 E-MTAB-2805:S_cell5 E-MTAB-2805:S_cell5 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527296 SAMEA2699562 E-MTAB-2805:S_cell5 S_cell5 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538196 E-MTAB-2805:G2M_cell75 E-MTAB-2805:G2M_cell75 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527297 SAMEA2699563 E-MTAB-2805:G2M_cell75 G2M_cell75 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538197 E-MTAB-2805:S_cell90 E-MTAB-2805:S_cell90 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527298 SAMEA2699564 E-MTAB-2805:S_cell90 S_cell90 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538273 E-MTAB-2805:G1_cell26 E-MTAB-2805:G1_cell26 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527374 SAMEA2699640 E-MTAB-2805:G1_cell26 G1_cell26 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538274 E-MTAB-2805:G2M_cell76 E-MTAB-2805:G2M_cell76 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527375 SAMEA2699641 E-MTAB-2805:G2M_cell76 G2M_cell76 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538275 E-MTAB-2805:G2M_cell64 E-MTAB-2805:G2M_cell64 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527376 SAMEA2699642 E-MTAB-2805:G2M_cell64 G2M_cell64 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538276 E-MTAB-2805:S_cell49 E-MTAB-2805:S_cell49 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527377 SAMEA2699643 E-MTAB-2805:S_cell49 S_cell49 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538277 E-MTAB-2805:G1_cell52 E-MTAB-2805:G1_cell52 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527378 SAMEA2699644 E-MTAB-2805:G1_cell52 G1_cell52 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538353 E-MTAB-2805:G1_cell80 E-MTAB-2805:G1_cell80 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527454 SAMEA2699720 E-MTAB-2805:G1_cell80 G1_cell80 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538354 E-MTAB-2805:G1_cell13 E-MTAB-2805:G1_cell13 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527455 SAMEA2699721 E-MTAB-2805:G1_cell13 G1_cell13 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538355 E-MTAB-2805:G1_cell24 E-MTAB-2805:G1_cell24 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527456 SAMEA2699722 E-MTAB-2805:G1_cell24 G1_cell24 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538356 E-MTAB-2805:G2M_cell35 E-MTAB-2805:G2M_cell35 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527457 SAMEA2699723 E-MTAB-2805:G2M_cell35 G2M_cell35 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538357 E-MTAB-2805:S_cell46 E-MTAB-2805:S_cell46 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527458 SAMEA2699724 E-MTAB-2805:S_cell46 S_cell46 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538142 E-MTAB-2805:G2M_cell44 E-MTAB-2805:G2M_cell44 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527243 SAMEA2699509 E-MTAB-2805:G2M_cell44 G2M_cell44 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538143 E-MTAB-2805:S_cell20 E-MTAB-2805:S_cell20 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527244 SAMEA2699510 E-MTAB-2805:S_cell20 S_cell20 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538144 E-MTAB-2805:G1_cell37 E-MTAB-2805:G1_cell37 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527245 SAMEA2699511 E-MTAB-2805:G1_cell37 G1_cell37 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538145 E-MTAB-2805:G1_cell66 E-MTAB-2805:G1_cell66 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527246 SAMEA2699512 E-MTAB-2805:G1_cell66 G1_cell66 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538146 E-MTAB-2805:G2M_cell4 E-MTAB-2805:G2M_cell4 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527247 SAMEA2699513 E-MTAB-2805:G2M_cell4 G2M_cell4 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538198 E-MTAB-2805:G1_cell59 E-MTAB-2805:G1_cell59 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527299 SAMEA2699565 E-MTAB-2805:G1_cell59 G1_cell59 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538199 E-MTAB-2805:S_cell60 E-MTAB-2805:S_cell60 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527300 SAMEA2699566 E-MTAB-2805:S_cell60 S_cell60 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538200 E-MTAB-2805:G1_cell67 E-MTAB-2805:G1_cell67 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527301 SAMEA2699567 E-MTAB-2805:G1_cell67 G1_cell67 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538201 E-MTAB-2805:G1_cell33 E-MTAB-2805:G1_cell33 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527302 SAMEA2699568 E-MTAB-2805:G1_cell33 G1_cell33 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538202 E-MTAB-2805:S_cell53 E-MTAB-2805:S_cell53 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527303 SAMEA2699569 E-MTAB-2805:S_cell53 S_cell53 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538278 E-MTAB-2805:G2M_cell15 E-MTAB-2805:G2M_cell15 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527379 SAMEA2699645 E-MTAB-2805:G2M_cell15 G2M_cell15 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538279 E-MTAB-2805:G1_cell68 E-MTAB-2805:G1_cell68 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527380 SAMEA2699646 E-MTAB-2805:G1_cell68 G1_cell68 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538280 E-MTAB-2805:S_cell52 E-MTAB-2805:S_cell52 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527381 SAMEA2699647 E-MTAB-2805:S_cell52 S_cell52 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538281 E-MTAB-2805:G2M_cell51 E-MTAB-2805:G2M_cell51 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527382 SAMEA2699648 E-MTAB-2805:G2M_cell51 G2M_cell51 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538282 E-MTAB-2805:S_cell22 E-MTAB-2805:S_cell22 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527383 SAMEA2699649 E-MTAB-2805:S_cell22 S_cell22 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538358 E-MTAB-2805:S_cell94 E-MTAB-2805:S_cell94 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527459 SAMEA2699725 E-MTAB-2805:S_cell94 S_cell94 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538359 E-MTAB-2805:S_cell55 E-MTAB-2805:S_cell55 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527460 SAMEA2699726 E-MTAB-2805:S_cell55 S_cell55 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538360 E-MTAB-2805:G1_cell95 E-MTAB-2805:G1_cell95 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527461 SAMEA2699727 E-MTAB-2805:G1_cell95 G1_cell95 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538361 E-MTAB-2805:S_cell78 E-MTAB-2805:S_cell78 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527462 SAMEA2699728 E-MTAB-2805:S_cell78 S_cell78 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538362 E-MTAB-2805:S_cell93 E-MTAB-2805:S_cell93 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527463 SAMEA2699729 E-MTAB-2805:S_cell93 S_cell93 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538147 E-MTAB-2805:S_cell13 E-MTAB-2805:S_cell13 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527248 SAMEA2699514 E-MTAB-2805:S_cell13 S_cell13 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538148 E-MTAB-2805:G1_cell88 E-MTAB-2805:G1_cell88 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527249 SAMEA2699515 E-MTAB-2805:G1_cell88 G1_cell88 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538149 E-MTAB-2805:S_cell27 E-MTAB-2805:S_cell27 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527250 SAMEA2699516 E-MTAB-2805:S_cell27 S_cell27 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538150 E-MTAB-2805:G2M_cell54 E-MTAB-2805:G2M_cell54 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527251 SAMEA2699517 E-MTAB-2805:G2M_cell54 G2M_cell54 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538151 E-MTAB-2805:G2M_cell17 E-MTAB-2805:G2M_cell17 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527252 SAMEA2699518 E-MTAB-2805:G2M_cell17 G2M_cell17 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538203 E-MTAB-2805:S_cell81 E-MTAB-2805:S_cell81 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527304 SAMEA2699570 E-MTAB-2805:S_cell81 S_cell81 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538204 E-MTAB-2805:G1_cell75 E-MTAB-2805:G1_cell75 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527305 SAMEA2699571 E-MTAB-2805:G1_cell75 G1_cell75 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538205 E-MTAB-2805:S_cell4 E-MTAB-2805:S_cell4 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527306 SAMEA2699572 E-MTAB-2805:S_cell4 S_cell4 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538206 E-MTAB-2805:S_cell72 E-MTAB-2805:S_cell72 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527307 SAMEA2699573 E-MTAB-2805:S_cell72 S_cell72 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538207 E-MTAB-2805:S_cell23 E-MTAB-2805:S_cell23 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527308 SAMEA2699574 E-MTAB-2805:S_cell23 S_cell23 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538283 E-MTAB-2805:S_cell85 E-MTAB-2805:S_cell85 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527384 SAMEA2699650 E-MTAB-2805:S_cell85 S_cell85 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538284 E-MTAB-2805:G1_cell1 E-MTAB-2805:G1_cell1 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527385 SAMEA2699651 E-MTAB-2805:G1_cell1 G1_cell1 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538285 E-MTAB-2805:S_cell11 E-MTAB-2805:S_cell11 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527386 SAMEA2699652 E-MTAB-2805:S_cell11 S_cell11 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538286 E-MTAB-2805:G1_cell28 E-MTAB-2805:G1_cell28 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527387 SAMEA2699653 E-MTAB-2805:G1_cell28 G1_cell28 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538287 E-MTAB-2805:S_cell56 E-MTAB-2805:S_cell56 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527388 SAMEA2699654 E-MTAB-2805:S_cell56 S_cell56 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538363 E-MTAB-2805:S_cell64 E-MTAB-2805:S_cell64 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527464 SAMEA2699730 E-MTAB-2805:S_cell64 S_cell64 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538364 E-MTAB-2805:G1_cell70 E-MTAB-2805:G1_cell70 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527465 SAMEA2699731 E-MTAB-2805:G1_cell70 G1_cell70 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538365 E-MTAB-2805:S_cell6 E-MTAB-2805:S_cell6 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527466 SAMEA2699732 E-MTAB-2805:S_cell6 S_cell6 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538366 E-MTAB-2805:S_cell37 E-MTAB-2805:S_cell37 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527467 SAMEA2699733 E-MTAB-2805:S_cell37 S_cell37 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538367 E-MTAB-2805:S_cell50 E-MTAB-2805:S_cell50 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527468 SAMEA2699734 E-MTAB-2805:S_cell50 S_cell50 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538152 E-MTAB-2805:G2M_cell26 E-MTAB-2805:G2M_cell26 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527253 SAMEA2699519 E-MTAB-2805:G2M_cell26 G2M_cell26 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538153 E-MTAB-2805:G2M_cell91 E-MTAB-2805:G2M_cell91 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527254 SAMEA2699520 E-MTAB-2805:G2M_cell91 G2M_cell91 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538154 E-MTAB-2805:G1_cell76 E-MTAB-2805:G1_cell76 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527255 SAMEA2699521 E-MTAB-2805:G1_cell76 G1_cell76 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538155 E-MTAB-2805:G2M_cell21 E-MTAB-2805:G2M_cell21 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527256 SAMEA2699522 E-MTAB-2805:G2M_cell21 G2M_cell21 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538156 E-MTAB-2805:S_cell96 E-MTAB-2805:S_cell96 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527257 SAMEA2699523 E-MTAB-2805:S_cell96 S_cell96 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538208 E-MTAB-2805:G2M_cell43 E-MTAB-2805:G2M_cell43 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527309 SAMEA2699575 E-MTAB-2805:G2M_cell43 G2M_cell43 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538209 E-MTAB-2805:G1_cell47 E-MTAB-2805:G1_cell47 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527310 SAMEA2699576 E-MTAB-2805:G1_cell47 G1_cell47 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538210 E-MTAB-2805:G1_cell9 E-MTAB-2805:G1_cell9 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527311 SAMEA2699577 E-MTAB-2805:G1_cell9 G1_cell9 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538211 E-MTAB-2805:S_cell66 E-MTAB-2805:S_cell66 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527312 SAMEA2699578 E-MTAB-2805:S_cell66 S_cell66 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538212 E-MTAB-2805:S_cell59 E-MTAB-2805:S_cell59 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527313 SAMEA2699579 E-MTAB-2805:S_cell59 S_cell59 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538288 E-MTAB-2805:G2M_cell80 E-MTAB-2805:G2M_cell80 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527389 SAMEA2699655 E-MTAB-2805:G2M_cell80 G2M_cell80 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538289 E-MTAB-2805:G2M_cell86 E-MTAB-2805:G2M_cell86 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527390 SAMEA2699656 E-MTAB-2805:G2M_cell86 G2M_cell86 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538290 E-MTAB-2805:G2M_cell56 E-MTAB-2805:G2M_cell56 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527391 SAMEA2699657 E-MTAB-2805:G2M_cell56 G2M_cell56 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538291 E-MTAB-2805:G2M_cell89 E-MTAB-2805:G2M_cell89 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527392 SAMEA2699658 E-MTAB-2805:G2M_cell89 G2M_cell89 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538292 E-MTAB-2805:G2M_cell31 E-MTAB-2805:G2M_cell31 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527393 SAMEA2699659 E-MTAB-2805:G2M_cell31 G2M_cell31 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538368 E-MTAB-2805:G2M_cell25 E-MTAB-2805:G2M_cell25 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527469 SAMEA2699735 E-MTAB-2805:G2M_cell25 G2M_cell25 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538369 E-MTAB-2805:G2M_cell12 E-MTAB-2805:G2M_cell12 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527470 SAMEA2699736 E-MTAB-2805:G2M_cell12 G2M_cell12 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G2/M ERX538370 E-MTAB-2805:S_cell68 E-MTAB-2805:S_cell68 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527471 SAMEA2699737 E-MTAB-2805:S_cell68 S_cell68 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S ERX538371 E-MTAB-2805:G1_cell32 E-MTAB-2805:G1_cell32 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527472 SAMEA2699738 E-MTAB-2805:G1_cell32 G1_cell32 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage G1 ERX538372 E-MTAB-2805:S_cell32 E-MTAB-2805:S_cell32 ERP006670 E-MTAB-2805 Gene expression pattern of single mES cells during cell cycle stages ERS527473 SAMEA2699739 E-MTAB-2805:S_cell32 S_cell32 RNA-Seq TRANSCRIPTOMIC cDNA mESC were grown in standard 2i media. The media composition was N2B27 basal media (NDiff 227, StemCells), 100 U/ml recombinant human leukemia inhibitory factor (Millipore), 1M PD0325901 (Stemgent), 3M CHIR99021 (Stemgent). For sorting of cell cycle fractions (G1, S and G2M), cells were trypisinized and stained with Hoechst 33342 (5_M) for 30min at 37C. Cells were sorted based on Hoechst staining for G1, S and G2M stages of cell cycle. For each cell cycle fraction, 3000 cells were loaded onto a 10-17 micron Fluidigm C1 Single-Cell Auto Prep IFC and cell capture was performed as per manufacturers protocol. Single cell capture, lysis, Reverse transcription and cDNA amplification are performed using the SMARTer cDNA synthesis kit (Clonetech) and Advantage2PCR kit (Clonetech) with 1:100 ratio of spike in (Ambion), within the IFC inside the C1-Autoprep system as per manufacturers protocol. Harvested cDNA from single cells after C1-Autoprep system run were used to make single cell libraries using Nextera XT DNA sample preparation kit (Illumina) utilising 96 dual barcoded indices. Library poolup was performed using AMPure XP beads (Agencourt Biosciences) and single cell libraries were sent for paired end sequencing at the Wellcome Trust Sequencing facility 100 0 F Application Read Forward 1 1 R Application Read Reverse 101 Illumina HiSeq 2000 Experimental Factor: cell cycle stage S