ERS2993924 SAMEA5186425 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186425 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 1 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 1 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993925 SAMEA5186426 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186426 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 10 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 10 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993926 SAMEA5186427 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186427 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 11 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 11 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993927 SAMEA5186428 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186428 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 12 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 12 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993928 SAMEA5186429 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186429 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 13 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 13 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993929 SAMEA5186430 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186430 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 14 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 14 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993930 SAMEA5186431 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186431 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 15 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 15 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993931 SAMEA5186432 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186432 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 16 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 16 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993932 SAMEA5186433 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186433 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 17 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 17 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993933 SAMEA5186434 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186434 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 18 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 18 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993934 SAMEA5186435 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186435 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 19 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 19 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993935 SAMEA5186436 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186436 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 2 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 2 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993936 SAMEA5186437 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186437 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 20 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 20 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993937 SAMEA5186438 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186438 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 21 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 21 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993938 SAMEA5186439 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186439 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 22 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 22 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993939 SAMEA5186440 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186440 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 23 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 23 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993940 SAMEA5186441 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186441 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 24 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 24 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993941 SAMEA5186442 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186442 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 25 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 25 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993942 SAMEA5186443 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186443 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 26 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 26 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993943 SAMEA5186444 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186444 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 27 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 27 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993944 SAMEA5186445 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:10Z External Id SAMEA5186445 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:10Z INSDC status public Submitter Id E-MTAB-7403:Sample 28 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 28 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993945 SAMEA5186446 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186446 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 29 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 29 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993946 SAMEA5186447 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186447 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 3 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 3 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993947 SAMEA5186448 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186448 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 30 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 30 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993948 SAMEA5186449 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186449 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 31 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 31 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993949 SAMEA5186450 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186450 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 32 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 32 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993950 SAMEA5186451 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186451 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 33 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 33 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993951 SAMEA5186452 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186452 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 34 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 34 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993952 SAMEA5186453 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186453 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 35 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 35 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993953 SAMEA5186454 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186454 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 36 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 36 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993954 SAMEA5186455 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186455 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 37 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 37 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993955 SAMEA5186456 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186456 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 38 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 38 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993956 SAMEA5186457 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186457 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 39 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 39 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993957 SAMEA5186458 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186458 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 4 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 4 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993958 SAMEA5186459 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186459 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 40 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 40 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993959 SAMEA5186460 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186460 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 5 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 5 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993960 SAMEA5186461 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186461 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 6 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 6 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993961 SAMEA5186462 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186462 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 7 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 7 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993962 SAMEA5186463 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186463 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 8 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 8 scientific_name Mus musculus strain C57BL/6 x CD1 ERS2993963 SAMEA5186464 10090 Mus musculus Protocols: Embryos of the appropriate stage were dissected in fresh M2 medium (Sigma-Aldrich), keeping the yolk sac intact. Embryos were considered to be at the LHT stage once both sides of the cardiac crescent were completely folded and fused. Linear heart tubes were micro-dissected using tungsten needles, keeping the overlying endoderm intact. Samples were dissociated into single-cells using 200μl Accutase (ThermoFisher) for 12 minutes at 37C, being agitated every 2 minutes before adding 200μl heat-inactivated FBS (ThermoFisher) to quench the reaction. Cells were then centrifuged at 1000rpm for 3 minutes at 40C before being suspended in 100μl HBSS (ThermoFisher) + 1% FBS and stored on ice. Single-cells were collected using a Sony SH800 FACS machine using a stringent single-cell collection protocol and sorted into 384 well plates containing SMART-seq2 lysis buffer 31 plus ERCC spike-ins at a concentration of 1:10million. To ensure good quality cells were collected a live/dead dye 438 (Abcam) was used; 100μl was added to the cell suspension at a 2x concentration in HBSS 10 minutes before collection, live cells were collected based on their FITC intensity. Once cells were collected, plates were sealed, spun down, and frozen using dry ice before being stored at -80C. There was no presequencing visual checks on the sorted cells. QC was performed on the sequencing data to exclude poor quality libraries:any samples with fewer than 50,000 total reads mapped to exons; less than 6,000 detected genes; more than 30% of reads mapped to ERCC spike-ins; or more than 15% of reads mapped to mitochondrial genes were excluded from the dataset. mRNA from single cells was isolated and amplified (25 PCR cycles) using the SMART-seq2 protocol. Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol. ENA-FIRST-PUBLIC 2019-06-01T04:02:53Z ENA-LAST-UPDATE 2018-12-17T16:09:11Z External Id SAMEA5186464 INSDC center name CANCER RESEARCH UK CAMBRIDGE INSTITUTE INSDC first public 2019-06-01T04:02:53Z INSDC last update 2018-12-17T16:09:11Z INSDC status public Submitter Id E-MTAB-7403:Sample 9 age embryonic day 8.25 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual 1 organism part heart tube sample name E-MTAB-7403:Sample 9 scientific_name Mus musculus strain C57BL/6 x CD1