SRX203377 GSM1033636_1 SRP017131 GSE42152 SRS374624 ChIP-Seq GENOMIC ChIP Illumina Genome Analyzer IIx GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033636 gds 301033636 GEO Accession GSM1033636 SRX203378 GSM1033637_1 SRP017131 GSE42152 SRS374625 ChIP-Seq GENOMIC ChIP Illumina Genome Analyzer IIx GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033637 gds 301033637 GEO Accession GSM1033637 SRX203379 GSM1033638_1 SRP017131 GSE42152 SRS374626 ChIP-Seq GENOMIC ChIP Illumina HiSeq 2000 GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033638 gds 301033638 GEO Accession GSM1033638 SRX203380 GSM1033639_1 SRP017131 GSE42152 SRS374627 ChIP-Seq GENOMIC ChIP Illumina HiSeq 2000 GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033639 gds 301033639 GEO Accession GSM1033639 SRX203381 GSM1033640_1 SRP017131 GSE42152 SRS374628 ChIP-Seq GENOMIC ChIP Illumina Genome Analyzer IIx GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033640 gds 301033640 GEO Accession GSM1033640 SRX203382 GSM1033641_1 SRP017131 GSE42152 SRS374629 ChIP-Seq GENOMIC ChIP Illumina Genome Analyzer IIx GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033641 gds 301033641 GEO Accession GSM1033641 SRX203383 GSM1033642_1 SRP017131 GSE42152 SRS374630 ChIP-Seq GENOMIC ChIP Illumina HiSeq 2000 GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033642 gds 301033642 GEO Accession GSM1033642 SRX203384 GSM1033643_1 SRP017131 GSE42152 SRS374631 ChIP-Seq GENOMIC ChIP Illumina HiSeq 2000 GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033643 gds 301033643 GEO Accession GSM1033643 SRX203385 GSM1033644_1 SRP017131 GSE42152 SRS374632 ChIP-Seq GENOMIC ChIP Illumina HiSeq 2000 GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033644 gds 301033644 GEO Accession GSM1033644 SRX203386 GSM1033645_1 SRP017131 GSE42152 SRS374633 ChIP-Seq GENOMIC ChIP Illumina HiSeq 2000 GEO Sample http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1033645 gds 301033645 GEO Accession GSM1033645 SRX335055 GSM1207786 SRP017131 GSE42152 SRS469949 GSM1207786 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina Genome Analyzer IIx GEO Sample GSM1207786 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207786 gds 301207786 GEO Accession GSM1207786 SRX335056 GSM1207787 SRP017131 GSE42152 SRS469950 GSM1207787 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207787 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207787 gds 301207787 GEO Accession GSM1207787 SRX335057 GSM1207788 SRP017131 GSE42152 SRS469951 GSM1207788 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207788 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207788 gds 301207788 GEO Accession GSM1207788 SRX335058 GSM1207789 SRP017131 GSE42152 SRS469952 GSM1207789 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207789 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207789 gds 301207789 GEO Accession GSM1207789 SRX335059 GSM1207790 SRP017131 GSE42152 SRS469953 GSM1207790 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207790 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207790 gds 301207790 GEO Accession GSM1207790 SRX335060 GSM1207791 SRP017131 GSE42152 SRS469954 GSM1207791 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207791 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207791 gds 301207791 GEO Accession GSM1207791 SRX335061 GSM1207792 SRP017131 GSE42152 SRS469956 GSM1207792 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207792 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207792 gds 301207792 GEO Accession GSM1207792 SRX335062 GSM1207793 SRP017131 GSE42152 SRS469955 GSM1207793 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207793 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207793 gds 301207793 GEO Accession GSM1207793 SRX335063 GSM1207794 SRP017131 GSE42152 SRS469957 GSM1207794 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 GEO Sample GSM1207794 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1207794 gds 301207794 GEO Accession GSM1207794 SRX2013615 GSM2271337 SRP017131 SRS1610589 GSM2271337 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 gds 302271337 GEO Accession GSM2271337 SRX2013616 GSM2271341 SRP017131 SRS1610590 GSM2271341 ChIP-Seq GENOMIC ChIP Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina protocol. Illumina HiSeq 2000 gds 302271341 GEO Accession GSM2271341