ERS3200771 SAMEA5394413 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394413 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 21 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 21 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200772 SAMEA5394414 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394414 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 24 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 24 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200773 SAMEA5394415 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394415 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 3 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 3 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200774 SAMEA5394416 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394416 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 31 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 31 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200775 SAMEA5394417 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394417 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 37 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 37 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200776 SAMEA5394419 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394419 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 41 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 41 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200777 SAMEA5394420 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394420 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 59 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 59 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200778 SAMEA5394421 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394421 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 7 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 7 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200779 SAMEA5394422 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394422 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 72 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 72 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200780 SAMEA5394423 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394423 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 73 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 73 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200781 SAMEA5394424 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394424 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 75 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 75 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200782 SAMEA5394425 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394425 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 83 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 83 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200783 SAMEA5394426 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394426 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 85 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 85 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200784 SAMEA5394427 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394427 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 88 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 88 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200785 SAMEA5394428 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394428 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 89 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 89 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200786 SAMEA5394429 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394429 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 9 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 9 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200787 SAMEA5394430 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394430 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 91 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 91 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200788 SAMEA5394431 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394431 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 95 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality fail sample name E-MTAB-6987:Sample 95 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200789 SAMEA5394432 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394432 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 1 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 1 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200790 SAMEA5394433 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394433 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 10 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 10 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200791 SAMEA5394434 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394434 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 11 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 11 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200792 SAMEA5394435 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394435 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 12 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 12 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200793 SAMEA5394436 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394436 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 13 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 13 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200794 SAMEA5394437 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394437 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 14 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 14 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200795 SAMEA5394438 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394438 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 15 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 15 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200796 SAMEA5394439 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394439 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 16 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 16 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200797 SAMEA5394440 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394440 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 17 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 17 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200798 SAMEA5394441 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394441 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 18 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 18 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200799 SAMEA5394442 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394442 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 19 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 19 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200800 SAMEA5394443 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394443 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 2 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 2 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200801 SAMEA5394444 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394444 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 20 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 20 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200802 SAMEA5394445 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394445 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 22 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 22 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200803 SAMEA5394446 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394446 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 23 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 23 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200804 SAMEA5394447 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394447 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 25 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 25 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200805 SAMEA5394448 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394448 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 26 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 26 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200806 SAMEA5394449 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394449 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 27 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 27 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200807 SAMEA5394450 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394450 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 28 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 28 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200808 SAMEA5394451 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394451 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 29 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 29 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200809 SAMEA5394452 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394452 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 30 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 30 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200810 SAMEA5394453 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394453 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 32 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 32 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200811 SAMEA5394454 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394454 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 33 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 33 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200812 SAMEA5394455 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394455 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 34 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 34 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200813 SAMEA5394456 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394456 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 35 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 35 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200814 SAMEA5394457 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394457 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 36 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 36 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200815 SAMEA5394458 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:23Z External Id SAMEA5394458 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:23Z INSDC status public Submitter Id E-MTAB-6987:Sample 38 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 38 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200816 SAMEA5394459 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394459 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 39 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 39 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200817 SAMEA5394460 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394460 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 4 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 4 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200818 SAMEA5394461 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394461 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 40 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 40 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200819 SAMEA5394462 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394462 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 42 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 42 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200820 SAMEA5394463 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394463 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 43 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 43 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200821 SAMEA5394464 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394464 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 44 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 44 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200822 SAMEA5394465 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394465 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 45 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 45 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200823 SAMEA5394466 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394466 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 46 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 46 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200824 SAMEA5394467 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394467 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 47 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 47 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200825 SAMEA5394468 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394468 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 48 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 48 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200826 SAMEA5394469 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394469 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 49 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 49 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200827 SAMEA5394470 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394470 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 5 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 5 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200828 SAMEA5394471 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394471 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 50 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 50 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200829 SAMEA5394472 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394472 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 51 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 51 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200830 SAMEA5394473 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394473 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 52 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 52 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200831 SAMEA5394474 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394474 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 53 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 53 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200832 SAMEA5394475 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394475 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 54 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 54 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200833 SAMEA5394476 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394476 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 55 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 55 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200834 SAMEA5394477 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394477 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 56 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 56 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200835 SAMEA5394478 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394478 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 57 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 57 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200836 SAMEA5394479 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394479 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 58 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 58 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200837 SAMEA5394480 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394480 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 6 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 6 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200838 SAMEA5394481 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394481 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 60 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 60 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200839 SAMEA5394482 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394482 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 61 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 61 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200840 SAMEA5394483 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394483 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 62 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 62 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200841 SAMEA5394484 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394484 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 63 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 63 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200842 SAMEA5394485 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394485 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 64 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 64 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200843 SAMEA5394486 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394486 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 65 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 65 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200844 SAMEA5394487 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394487 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 66 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 66 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200845 SAMEA5394488 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394488 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 67 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 67 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200846 SAMEA5394489 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394489 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 68 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 68 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200847 SAMEA5394490 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394490 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 69 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 69 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200848 SAMEA5394491 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394491 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 70 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 70 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200849 SAMEA5394492 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394492 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 71 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 71 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200850 SAMEA5394493 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394493 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 74 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 74 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200851 SAMEA5394494 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394494 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 76 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 76 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200852 SAMEA5394495 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394495 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 77 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 77 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200853 SAMEA5394496 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394496 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 78 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 78 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200854 SAMEA5394497 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394497 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 79 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 79 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200855 SAMEA5394498 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:28Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394498 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:28Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 8 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 8 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200856 SAMEA5394499 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394499 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 80 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 80 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200857 SAMEA5394500 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394500 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 81 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 81 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200858 SAMEA5394501 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394501 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 82 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 82 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200859 SAMEA5394502 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394502 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 84 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 84 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200860 SAMEA5394503 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:24Z External Id SAMEA5394503 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:24Z INSDC status public Submitter Id E-MTAB-6987:Sample 86 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 86 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200861 SAMEA5394504 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:25Z External Id SAMEA5394504 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:25Z INSDC status public Submitter Id E-MTAB-6987:Sample 87 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 87 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200862 SAMEA5394505 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:25Z External Id SAMEA5394505 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:25Z INSDC status public Submitter Id E-MTAB-6987:Sample 90 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 90 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200863 SAMEA5394506 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:25Z External Id SAMEA5394506 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:25Z INSDC status public Submitter Id E-MTAB-6987:Sample 92 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 92 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200864 SAMEA5394507 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:25Z External Id SAMEA5394507 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:25Z INSDC status public Submitter Id E-MTAB-6987:Sample 93 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 93 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200865 SAMEA5394508 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:25Z External Id SAMEA5394508 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:25Z INSDC status public Submitter Id E-MTAB-6987:Sample 94 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 94 scientific_name Mus musculus sex mixed strain C57BL/6 ERS3200866 SAMEA5394509 10090 Mus musculus Protocols: Embryos from pregnant mice were collected at 10.5 days of pregnancy. A total of 15 embryos was dissected to isolate the aorta-gonad-mesonephros (AGM) region. The fifteen AGM samples were combined and stained with antibodies specific for VE-Cadherin (endothelial specific) and CD41(blood specific) cell surface markers. Cells expressing VE-Cadherin were sorted on a FACS sorter and loaded on a Fluidigm C1 10-17 uM IFC Chip. Annotation of cell capture was carried out on a brightfield microscope at 40x magnification and each captured site was noted for having single-cell capture, doublet cell capture or debris. A total of 83 chambers out of the 96 in the IFC chip contained single cells. Lysis, reverse transcription, and PCR reagents (Clontech Takara) were then loaded into appropriate inlets as per Fluidigm layout. ERCC spike-in controls (Ambion) were added at a dilution of 1:4000 within the lysis mix to gain limit of detection and normalisation in downstream analysis. Illumina library preparation was carried out using the Nextera XT DNA system (Illumina), but volumes were reduced as per the modified Fluidigm C1 protocol. Tagmentation was performed on all 96 samples using 1.25 ul of cDNA (125 pg total concentration) combined with 2.5 ul of tagmentation buffer (TD) and 1.25 ul of Amplicon Tagment Mix (ATM), and incubated for 10 min at 55 degrees. After incubation, 1.25 ul of Neutrilize Tagment Mix (NT) was added. Illumina PCR barcoded indexes were combined to obtain 96 distinct combinations of i7 and i5 barcodes, and 2.5 ul of combined index was added along with 3.75 ul of Nextera PCR Mix (NPM). Samples were then put through 12 cycles of PCR as per the Illumina protocol. Each column was then pooled into a 0.2 mL 8-strip PCR tube and Ampure XP purification was performed, after which each pool was combined to obtain a single 96-sample multiplexed pool of barcoded library. The final sequencing library was quantified by Qubit (Life Technologies) and size distribution was measured on an Agilent BioAnalyzer. ENA-FIRST-PUBLIC 2019-03-12T17:05:29Z ENA-LAST-UPDATE 2019-03-05T10:20:25Z External Id SAMEA5394509 INSDC center name WELLCOME TRUST SANGER INSTITUTE INSDC first public 2019-03-12T17:05:29Z INSDC last update 2019-03-05T10:20:25Z INSDC status public Submitter Id E-MTAB-6987:Sample 96 age embryonic day 10.5 broker name ArrayExpress common name house mouse developmental stage embryo disease normal genotype wild type genotype individual mixed pool of 15 embryos inferred cell type endothelial cell organism part splanchnic layer of lateral plate mesoderm phenotype VE-Cadherin positive post analysis well quality pass sample name E-MTAB-6987:Sample 96 scientific_name Mus musculus sex mixed strain C57BL/6