SRX698090 2oMEF-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS699221 2oMEF_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX698179 2oMEF-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699221 2oMEF_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX698338 2oMEF-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699221 2oMEF_ChIP_K4me3 ChIP-Seq GENOMIC ChIP 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX698339 2oMEF-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699221 2oMEF_ChIP_K27me3 ChIP-Seq GENOMIC ChIP 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX698340 2oMEF_ChIPseq_K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699221 2oMEF_ChIP_K36me3 ChIP-Seq GENOMIC ChIP 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX698341 2oMEF-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS699221 2oMEF_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX698345 D2H-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS698578 D2H_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX698945 D5H-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS698969 D2H_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699723 D8H-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS699871 SAMN03024093 D8H_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699740 D11H-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS699933 SAMN03024094 D11H_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699886 D16H-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700106 SAMN03024095 D2H_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699942 D18H-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700161 SAMN03024096 D18H_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699947 D16L-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700167 SAMN03024097 D16L_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699955 D21L-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700174 D21L_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699957 D21L0-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700232 SAMN03024099 D21L0_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699972 1oiPSC-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700253 SAMN03024100 1oiPSC_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699973 2oiPSC-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700254 SAMN03024101 2oiPSC_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX699976 rtTA_ESC-long RNAseq SRP046744 5μg total RNA was depleted of Ribosomal RNA using the Ribo-ZeroTMrRNA Removal Kit (Epicenter PN RZH110424) as per manufacturer’s instructions. The rRNA depleted RNA was then run on an Agilent RNA 6000 Pico Kit (PN 5067-1513) on the Agilent Bioanalyzer 2100 to confirm rRNA depletion. Sequencing libraries where generated from the rRNA depleted RNA using the SOLiDTM Transcriptome Multiplexing Kit (PN 4427046) from Applied Biosystems following the manufacturer’s publication. Final libraries were quantified and qualified using Agilent High Sensitivity DNA Kit (PN 5067-4626) on the Agilent Bioanalyzer 2100. Sequencing libraries were subsequently pooled in equimolar ratios (four libraries per pool) and clonally amplified onto SOLiD Nanobeads. Clonal amplification was completed via emulsion PCR using the SOLiD EZ Bead System (PN 4448419, 4448418 and 4448420) coupled with SOLiD EZ Bead N200 amplification reagents (PN 4467267, 4457185, 4467281, 4467283, 4467282). Following emulsion PCR clonally amplified Nanobeads were enriched using the SOLiD EZ Bead Enricher Kits (4467276, 4444140, 4453073) before being deposited into SOLiDTM 6-Lane FlowChip (PN 4461826) using the SOLiD Flowchip Deposition Kit v2 (PN 4468081) as per the manufacturer’s recommendations. SRS700256 SAMN03024102 rtTA_ESC_longRNA RNA-Seq TRANSCRIPTOMIC RANDOM 110 0 Application Read Forward 1 1 Application Read Reverse 76 AB 5500xl Genetic Analyzer SRX700580 D2H-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS698578 D2H_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700581 D5H-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS698969 D5H_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700582 D8H-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS699871 D8H_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700583 D11H-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS699933 D11H_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700584 D16H-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700106 D16H_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700585 D18H-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700161 D18H_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700605 D16L-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700167 D16L_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700606 D21L-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700174 D21L_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700607 D21L0-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700232 D21L0_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700608 1oiPSC-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700253 1oiPSC_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700609 2oiPSC-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700254 2oiPSC_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700610 rtTA_ESC-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700256 rtTA_ESC_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB SOLiD 4 System SRX700615 2oMEF_2-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700787 SAMN03024105 2oMEF_2_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB 5500 Genetic Analyzer SRX700616 D1H_2-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700788 SAMN03024106 D1H_2_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB 5500 Genetic Analyzer SRX700617 D2H_2-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700789 SAMN03024107 D2H_2_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB 5500 Genetic Analyzer SRX700618 D3H_2-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700790 SAMN03024108 D3H_2_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB 5500 Genetic Analyzer SRX700619 D4H_2-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700791 SAMN03024109 D4H_2_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB 5500 Genetic Analyzer SRX700620 D30_Fclass_c1-short RNAseq SRP046744 RNA was extracted from cells using the mirVana miRNA isolation kit (Ambion #1560) following the manufacturer’s instructions, and quality validated using on a Bioanalyser before sequence library preparation. Small RNA libraries for next generation sequencing (NGS) were prepared using the small RNA preparation protocol of the SOLiD® Total RNA-Seq kit as per the manufacturer’s instructions. Specifically, size selection was performed to include RNA between 18-38nt in length. SRS700792 SAMN03031941 D30_Fclass_c1_shortRNA miRNA-Seq TRANSCRIPTOMIC size fractionation 35 0 Application Read Forward 1 AB 5500 Genetic Analyzer SRX701213 D2H-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698578 D2H_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701216 D5H-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698969 D5H_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701220 D8H-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699871 D8H_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701222 D11H-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699933 D11H_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701224 D16H-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700106 D16H_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701227 D18H-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700161 D18H_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701229 D16L-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700167 D16L_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701308 D21L-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700174 D21L_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701323 D21L0-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700232 D21L0_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701335 1oiPSC-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700253 1oiPSC_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701337 2oiPSC-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700254 2oiPSC_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX701338 rtTA_ESC-ChIPseq-Input SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700256 rtTA_ESC_ChIP_Input ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP Input SRX707437 D2H-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698578 D2H_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707438 D5H-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698969 D5H_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707439 D8H-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699871 D8H_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707782 D11H-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699933 D11H_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707784 D16H-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700106 D16H_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707786 D18H-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700161 D18H_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707789 D16L-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700167 D16L_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707840 D21L-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700174 D21L_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707841 D21L0-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700232 D21L0_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX707843 1oiPSC-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700253 1oiPSC_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX708000 2oiPSC-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700254 2oiPSC_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX708001 rtTA_ESC-ChIPseq-K4me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700256 rtTA_ESC_ChIP_K4me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K4me3 SRX708099 D2H-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698578 D2H_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708100 D5H-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698969 D5H_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708101 D8H-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699871 D8H_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708103 D11H-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699933 D11H_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708104 D16H-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700106 D16H_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708112 D18H-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700161 D18H_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708113 D16L-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700167 D16L_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708116 D21L-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700174 D21L_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708117 D21L0-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700232 D21L0_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708118 1oiPSC-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700253 1oiPSC_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708119 2oiPSC-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700254 2oiPSC_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX708121 rtTA_ESC-ChIPseq-K27me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700256 rtTA_ESC_ChIP_K27me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K27me3 SRX709013 D2H-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698578 D2H_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709016 D5H-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS698969 D5H_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709017 D8H-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699871 D8H_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709018 D11H-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS699933 D11H_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709019 D16H-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700106 D16H_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709023 D18H-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700161 D18H_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709045 D16L-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700167 D16L_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709048 D21L-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700174 D21L_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709051 D21L0-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700232 D21L0_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709074 1oiPSC-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700253 1oiPSC_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709075 2oiPSC-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700254 2oiPSC_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3 SRX709191 rtTA_ESC-ChIPseq-K36me3 SRP046744 Sequencing libraries were prepared according to Illumina ChIP-seq Library Preparation kit instructions. 50ng of immunoprecipitated or input DNA was end-repaired, followed by the 3′ addition of a single adenosine nucleotide and ligation to universal library adapters. Ligated material was separated on a 2.0% agarose gel, followed by the excision of a 250–350bp fragment and column purification using Qiagen gel purification kit. DNA libraries were prepared by PCR amplification (18 cycles). SRS700256 rtTA_ESC_ChIP_K36me3 ChIP-Seq GENOMIC RANDOM 202 0 Application Read Forward 1 1 Application Read Reverse 102 Illumina HiSeq 2000 standard Illumina pipeline RTA 2.8.0 ChIP K36me3