SRX957573 GSM1634858 SRP056212 SRS874934 GSM1634858 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634858 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634858 gds 301634858 GEO Accession GSM1634858 SRX957574 GSM1634859 SRP056212 SRS874933 GSM1634859 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634859 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634859 gds 301634859 GEO Accession GSM1634859 SRX957575 GSM1634860 SRP056212 SRS874932 GSM1634860 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634860 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634860 gds 301634860 GEO Accession GSM1634860 SRX957576 GSM1634861 SRP056212 SRS874931 GSM1634861 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634861 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634861 gds 301634861 GEO Accession GSM1634861 SRX957577 GSM1634862 SRP056212 SRS874929 GSM1634862 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634862 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634862 gds 301634862 GEO Accession GSM1634862 SRX957578 GSM1634863 SRP056212 SRS874930 GSM1634863 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634863 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634863 gds 301634863 GEO Accession GSM1634863 SRX957579 GSM1634864 SRP056212 SRS874928 GSM1634864 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634864 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634864 gds 301634864 GEO Accession GSM1634864 SRX957580 GSM1634865 SRP056212 SRS874927 GSM1634865 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634865 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634865 gds 301634865 GEO Accession GSM1634865 SRX957581 GSM1634866 SRP056212 SRS874925 GSM1634866 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634866 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634866 gds 301634866 GEO Accession GSM1634866 SRX957582 GSM1634867 SRP056212 SRS874926 GSM1634867 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634867 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634867 gds 301634867 GEO Accession GSM1634867 SRX957583 GSM1634868 SRP056212 SRS874924 GSM1634868 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634868 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634868 gds 301634868 GEO Accession GSM1634868 SRX957584 GSM1634869 SRP056212 SRS874923 GSM1634869 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634869 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634869 gds 301634869 GEO Accession GSM1634869 SRX957585 GSM1634870 SRP056212 SRS874922 GSM1634870 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634870 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634870 gds 301634870 GEO Accession GSM1634870 SRX957586 GSM1634871 SRP056212 SRS874921 GSM1634871 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634871 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634871 gds 301634871 GEO Accession GSM1634871 SRX957587 GSM1634872 SRP056212 SRS874920 GSM1634872 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634872 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634872 gds 301634872 GEO Accession GSM1634872 SRX957588 GSM1634873 SRP056212 SRS874919 GSM1634873 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634873 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634873 gds 301634873 GEO Accession GSM1634873 SRX957589 GSM1634874 SRP056212 SRS874918 GSM1634874 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634874 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634874 gds 301634874 GEO Accession GSM1634874 SRX957590 GSM1634875 SRP056212 SRS874917 GSM1634875 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634875 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634875 gds 301634875 GEO Accession GSM1634875 SRX957591 GSM1634876 SRP056212 SRS874916 GSM1634876 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634876 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634876 gds 301634876 GEO Accession GSM1634876 SRX957592 GSM1634877 SRP056212 SRS874915 GSM1634877 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2500 GEO Sample GSM1634877 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634877 gds 301634877 GEO Accession GSM1634877 SRX957593 GSM1634878 SRP056212 SRS874914 GSM1634878 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634878 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634878 gds 301634878 GEO Accession GSM1634878 SRX957594 GSM1634879 SRP056212 SRS874913 GSM1634879 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634879 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634879 gds 301634879 GEO Accession GSM1634879 SRX957595 GSM1634880 SRP056212 SRS874912 GSM1634880 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634880 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634880 gds 301634880 GEO Accession GSM1634880 SRX957596 GSM1634881 SRP056212 SRS874911 GSM1634881 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634881 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634881 gds 301634881 GEO Accession GSM1634881 SRX957597 GSM1634882 SRP056212 SRS874910 GSM1634882 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634882 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634882 gds 301634882 GEO Accession GSM1634882 SRX957598 GSM1634883 SRP056212 SRS874909 GSM1634883 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634883 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634883 gds 301634883 GEO Accession GSM1634883 SRX957599 GSM1634884 SRP056212 SRS874908 GSM1634884 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634884 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634884 gds 301634884 GEO Accession GSM1634884 SRX957600 GSM1634885 SRP056212 SRS874907 GSM1634885 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634885 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634885 gds 301634885 GEO Accession GSM1634885 SRX957601 GSM1634886 SRP056212 SRS874906 GSM1634886 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634886 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634886 gds 301634886 GEO Accession GSM1634886 SRX957602 GSM1634887 SRP056212 SRS874905 GSM1634887 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634887 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634887 gds 301634887 GEO Accession GSM1634887 SRX957603 GSM1634888 SRP056212 SRS874904 GSM1634888 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634888 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634888 gds 301634888 GEO Accession GSM1634888 SRX957604 GSM1634889 SRP056212 SRS874903 GSM1634889 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634889 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634889 gds 301634889 GEO Accession GSM1634889 SRX957605 GSM1634890 SRP056212 SRS874902 GSM1634890 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634890 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634890 gds 301634890 GEO Accession GSM1634890 SRX957606 GSM1634891 SRP056212 SRS874900 GSM1634891 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634891 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634891 gds 301634891 GEO Accession GSM1634891 SRX957607 GSM1634892 SRP056212 SRS874901 GSM1634892 RNA-Seq TRANSCRIPTOMIC cDNA E11 AGM region (41-45 sp): ECs: CD31+VE-cadherin+CD41-CD43-CD45-Ter119-, T1 pre-HSCs: CD31+CD45-CD41lowc-Kit+CD201high, T2 pre-HSCs: CD31+CD45+CD41low; fetal liver: E12 HSCs: Lin-Sca-1+Mac-1lowCD201+, E14 HSCs: CD45+CD150+CD48-CD201+ FACS enriched cells were kept on ice until lysed and reverse transcribed. Morphologically deformed cells were discarded. Single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette. For the 10-cell pool, individual cells were collected in PBS-BSA, and then transferred together into cell lysis buffer in less than 3 aspiration cycles to minimize the carryover. 0.05 μl of 1:200,000 dilution of ERCC RNA spike-in Mix1 (Ambion) were added to lysis buffer per reaction. The cDNA libraries from single cells or 10-cell pools were generated as described previously (Nature methods, 2009). 50-200 ng amplified single-cell or 10-cell-pool cDNA were sonicated to ~250 bp fragments by Covaris S2 system, and libraries were generated using NEB DNA Library Preparation Kit following the manufacture’s protocol. Illumina HiSeq 2000 GEO Sample GSM1634892 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1634892 gds 301634892 GEO Accession GSM1634892