Source Name Comment [ENA_SAMPLE] Comment [Sample_description] Comment [Sample_source_name] Comment [Sample_title] Characteristics [age] Characteristics [antibody] Characteristics [antibody quantity] Characteristics [bead volume] Characteristics [cells used] Characteristics [estimated fragment size] Characteristics [genotype] Characteristics [magnetic beads] Characteristics [organism] Term Source REF Term Accession Number Characteristics [strain] Term Source REF Term Accession Number Protocol REF Term Source REF Protocol REF Term Source REF Extract Name Comment [INSTRUMENT_MODEL] Comment [LIBRARY_LAYOUT] Comment [LIBRARY_SELECTION] Comment [LIBRARY_SOURCE] Comment [LIBRARY_STRATEGY] Material Type Assay Name Comment [ENA_EXPERIMENT] Comment [Platform_title] Technology Type Protocol REF Term Source REF Scan Name Comment [ENA_RUN] Comment [FASTQ_URI] Derived Array Data File Comment [Derived ArrayExpress FTP file] FactorValue [ANTIBODY] FactorValue [ANTIBODY QUANTITY] FactorValue [BEAD VOLUME] FactorValue [CELLS USED] FactorValue [ESTIMATED FRAGMENT SIZE] FactorValue [GENOTYPE] FactorValue [MAGNETIC BEADS] GSM1360737 1 SRS584679 Sample 20 primary CD4+ CD8+ DP thymocytes DP E47 5-6 weeks Santa Cruz (SC-349X) 10 �g 25�l 1.0E+07 94bp WT Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360737 extract 1 AB SOLiD 4 System SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360737 SRX505083 AB SOLiD 4 System (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210617 SRR1210617 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/007/SRR1210617/SRR1210617.fastq.gz GSM1360737_DP_E47_1_10Mcells_TAGC.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.1.zip Santa Cruz (SC-349X) 10 �g 25�l 1.0E+07 94bp WT Protein G dynabeads GSM1360736 1 SRS584678 Sample 19 primary Rag2 -/- thymocytes Rag2 -/- Input 5-6 weeks N/A N/A NA 1.7E+06 208bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360736 extract 1 Illumina HiSeq 2000 SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360736 SRX505082 Illumina HiSeq 2000 (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210616 SRR1210616 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/006/SRR1210616/SRR1210616.fastq.gz GSM1360736_D1U1YACXX_1_0_1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.1.zip N/A N/A NA 1.7E+06 208bp Rag2 -/- Protein G dynabeads GSM1360735 1 SRS584677 Sample 18 primary Rag2 -/- thymocytes Rag2 -/- Runx1 5-6 weeks Abcam (ab23980) 10 �g 25�l 1.0E+07 125bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360735 extract 1 AB 5500xl Genetic Analyzer SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360735 SRX505081 AB 5500xl Genetic Analyzer (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210615 SRR1210615 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/005/SRR1210615/SRR1210615.fastq.gz GSM1360735_Rag_RUNX1_1_TAGC.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.1.zip Abcam (ab23980) 10 �g 25�l 1.0E+07 125bp Rag2 -/- Protein G dynabeads GSM1360734 1 SRS584676 Sample 17 primary Rag2 -/- thymocytes Rag2 -/- H3K36me3 ChIP-Seq biorep 2 techrep 2 5-6 weeks Abcam (ab9050) 2 �g 20�l 5.0E+06 206bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360734 extract 1 Illumina Genome Analyzer II SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360734 SRX505080 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210614 SRR1210614 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/004/SRR1210614/SRR1210614.fastq.gz GSM1360734_H3K36me3_Rag_rep2_2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.2.zip Abcam (ab9050) 2 �g 20�l 5.0E+06 206bp Rag2 -/- Protein G dynabeads GSM1360733 1 SRS584675 Sample 16 primary Rag2 -/- thymocytes Rag2 -/- H3K36me3 ChIP-Seq biorep 2 techrep 1 5-6 weeks Abcam (ab9050) 2 �g 20�l 5.0E+06 206bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360733 extract 1 Illumina Genome Analyzer II SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360733 SRX505079 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210613 SRR1210613 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/003/SRR1210613/SRR1210613.fastq.gz GSM1360733_H3K36me3_Rag_rep2_1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.2.zip Abcam (ab9050) 2 �g 20�l 5.0E+06 206bp Rag2 -/- Protein G dynabeads GSM1360732 1 SRS584681 Sample 15 primary Rag2 -/- thymocytes Rag2 -/- H3K36me3 ChIP-Seq biorep 1 5-6 weeks Abcam (ab9050) 2 �g 20�l 5.0E+06 206bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360732 extract 1 Illumina Genome Analyzer II SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360732 SRX505078 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210612 SRR1210612 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/002/SRR1210612/SRR1210612.fastq.gz GSM1360732_H3K36me3_Rag_rep1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.2.zip Abcam (ab9050) 2 �g 20�l 5.0E+06 206bp Rag2 -/- Protein G dynabeads GSM1360723 1 SRS584674 Sample 6 primary Rag2 -/- thymocytes Rag2 -/- H3K4me1 ChIP-Seq biorep 2 5-6 weeks Abcam (ab8895) 2 �g 20�l 5.0E+06 146bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360723 extract 1 Illumina Genome Analyzer II SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360723 SRX505077 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210611 SRR1210611 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/001/SRR1210611/SRR1210611.fastq.gz GSM1360723_H3K4me1_Rag_rep2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.2.zip Abcam (ab8895) 2 �g 20�l 5.0E+06 146bp Rag2 -/- Protein G dynabeads GSM1360722 1 SRS584672 Sample 5 primary Rag2 -/- thymocytes Rag2 -/- H3K4me1 ChIP-Seq biorep 1 5-6 weeks Abcam (ab8895) 2 �g 20�l 5.0E+06 146bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360722 extract 1 Illumina Genome Analyzer II SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360722 SRX505076 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210610 SRR1210610 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/000/SRR1210610/SRR1210610.fastq.gz GSM1360722_H3K4me1_Rag_rep1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.2.zip Abcam (ab8895) 2 �g 20�l 5.0E+06 146bp Rag2 -/- Protein G dynabeads GSM1360719 1 SRS584673 Sample 2 primary Rag2 -/- thymocytes Rag2 -/- Ets1 ChIP-Seq biorep 2 5-6 weeks Santa Cruz (sc-350x) 20 �g 200�l 1.0E+08 146bp Rag2 -/- Sheep anti-rabbit IgG dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360719 extract 1 Illumina Genome Analyzer II SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360719 SRX505075 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210609 SRR1210609 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/009/SRR1210609/SRR1210609.fastq.gz GSM1360719_Ets1_Rag_rep2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.3.zip Santa Cruz (sc-350x) 20 �g 200�l 1.0E+08 146bp Rag2 -/- Sheep anti-rabbit IgG dynabeads GSM1360718 1 SRS584671 Sample 1 primary Rag2 -/- thymocytes Rag2 -/- Ets1 ChIP-Seq biorep 1 5-6 weeks Santa Cruz (sc-350x) 20 �g 200�l 1.0E+08 136bp Rag2 -/- Sheep anti-rabbit IgG dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360718 extract 1 Illumina Genome Analyzer II SINGLE ChIP genomic ChIP-Seq genomic DNA GSM1360718 SRX505074 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress SRR1210608 SRR1210608 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/008/SRR1210608/SRR1210608.fastq.gz GSM1360718_Ets1_Rag_rep1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.3.zip Santa Cruz (sc-350x) 20 �g 200�l 1.0E+08 136bp Rag2 -/- Sheep anti-rabbit IgG dynabeads GSM1360731 1 Sample 14 primary Rag2 -/- thymocytes Rag2 -/- H3K27me3 ChIP-Seq biorep 2 techrep 2 5-6 weeks Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360731 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360731 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360731_H3K27me3_Rag_rep2_2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.3.zip Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads GSM1360730 1 Sample 13 primary Rag2 -/- thymocytes Rag2 -/- H3K27me3 ChIP-Seq biorep 2 techrep 1 5-6 weeks Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360730 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360730 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360730_H3K27me3_Rag_rep2_1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.3.zip Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads GSM1360729 1 Sample 12 primary Rag2 -/- thymocytes Rag2 -/- H3K27me3 ChIP-Seq biorep 1 techrep 2 5-6 weeks Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360729 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360729 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360729_H3K27me3_Rag_rep1_2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.4.zip Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads GSM1360728 1 Sample 11 primary Rag2 -/- thymocytes Rag2 -/- H3K27me3 ChIP-Seq biorep 1 techrep 1 5-6 weeks Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360728 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360728 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360728_H3K27me3_Rag_rep1_1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.4.zip Abcam (ab6002) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads GSM1360727 1 Sample 10 primary Rag2 -/- thymocytes Rag2 -/- H3K4me3 ChIP-Seq biorep 2 5-6 weeks Diagenode (pAb-003-050) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360727 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360727 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360727_H3K4me3_Rag_rep2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.4.zip Diagenode (pAb-003-050) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads GSM1360726 1 Sample 9 primary Rag2 -/- thymocytes Rag2 -/- H3K4me3 ChIP-Seq biorep 1 5-6 weeks Diagenode (pAb-003-050) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360726 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360726 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360726_H3K4me3_Rag_rep1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.4.zip Diagenode (pAb-003-050) 2 �g 20�l 5.0E+06 136bp Rag2 -/- Protein G dynabeads GSM1360725 1 Sample 8 primary Rag2 -/- thymocytes Rag2 -/- H3K4me2 ChIP-Seq biorep 2 5-6 weeks Abcam (ab32356) 2 �g 20�l 5.0E+06 126bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360725 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360725 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360725_H3K4me2_Rag_rep2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.4.zip Abcam (ab32356) 2 �g 20�l 5.0E+06 126bp Rag2 -/- Protein G dynabeads GSM1360724 1 Sample 7 primary Rag2 -/- thymocytes Rag2 -/- H3K4me2 ChIP-Seq biorep 1 5-6 weeks Abcam (ab32356) 2 �g 20�l 5.0E+06 126bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360724 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360724 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360724_H3K4me2_Rag_rep1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.5.zip Abcam (ab32356) 2 �g 20�l 5.0E+06 126bp Rag2 -/- Protein G dynabeads GSM1360721 1 Sample 4 primary Rag2 -/- thymocytes Rag2 -/- RNA Pol II (N20) ChIP-Seq biorep 2 5-6 weeks Santa Cruz (sc-899x) 5 �g 50�l 2.5E+07 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360721 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360721 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360721_Pol2_Rag_N20_rep2.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.5.zip Santa Cruz (sc-899x) 5 �g 50�l 2.5E+07 136bp Rag2 -/- Protein G dynabeads GSM1360720 1 Sample 3 primary Rag2 -/- thymocytes Rag2 -/- RNA Pol II (N20) ChIP-Seq biorep 1 5-6 weeks Santa Cruz (sc-899x) 5 �g 50�l 2.5E+07 136bp Rag2 -/- Protein G dynabeads Mus musculus EFO http://purl.obolibrary.org/obo/NCBITaxon_10090 C57BL/6 EFO EFO_0004472 P-GSE56393-1 ArrayExpress P-GSE56393-2 ArrayExpress GSM1360720 extract 1 Illumina Genome Analyzer II ChIP genomic ChIP-Seq genomic DNA GSM1360720 Illumina Genome Analyzer II (Mus musculus) sequencing assay P-GSE56393-3 ArrayExpress GSM1360720_Pol2_Rag_N20_rep1.wig ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-56393/E-GEOD-56393.processed.5.zip Santa Cruz (sc-899x) 5 �g 50�l 2.5E+07 136bp Rag2 -/- Protein G dynabeads