GSM1429903: ESC_Control_H3K9me3 (ctrl for KD1); Mus musculus; ChIP-Seq

SRX647886 GSM1429903 GSM1429903: ESC_Control_H3K9me3 (ctrl for KD1); Mus musculus; ChIP-Seq SRP044146 SRS655154 GSM1429903 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 GSM1429903 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429903 gds 301429903 GEO Accession GSM1429903 SRX647887 GSM1429904 GSM1429904: ESC_H33KD1_H3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS655155 GSM1429904 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 GSM1429904 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429904 gds 301429904 GEO Accession GSM1429904 SRX647888 GSM1429905 GSM1429905: ESC_Control_H33 (ctrl for KD1); Mus musculus; ChIP-Seq SRP044146 SRS655156 GSM1429905 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 GSM1429905 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429905 gds 301429905 GEO Accession GSM1429905 SRX647889 GSM1429906 GSM1429906: ESC_H33KD1_H33; Mus musculus; ChIP-Seq SRP044146 SRS655157 GSM1429906 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 GSM1429906 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429906 gds 301429906 GEO Accession GSM1429906 SRX647890 GSM1429907 GSM1429907: ESC_Control_H312 (ctrl for KD1); Mus musculus; ChIP-Seq SRP044146 SRS655158 GSM1429907 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 GSM1429907 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429907 gds 301429907 GEO Accession GSM1429907 SRX647891 GSM1429908 GSM1429908: ESC_H33KD1_H312; Mus musculus; ChIP-Seq SRP044146 SRS655159 GSM1429908 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 GSM1429908 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429908 gds 301429908 GEO Accession GSM1429908 SRX647892 GSM1429909 GSM1429909: ESC_Control_H3 (ctrl for KD1); Mus musculus; ChIP-Seq SRP044146 SRS655160 GSM1429909 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 GSM1429909 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429909 gds 301429909 GEO Accession GSM1429909 SRX647893 GSM1429910 GSM1429910: ESC_H33KD1_H3; Mus musculus; ChIP-Seq SRP044146 SRS655161 GSM1429910 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 GSM1429910 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429910 gds 301429910 GEO Accession GSM1429910 SRX647894 GSM1429911 GSM1429911: ESC_Control_nInput (ctrl for KD1); Mus musculus; ChIP-Seq SRP044146 SRS655162 GSM1429911 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 GSM1429911 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429911 gds 301429911 GEO Accession GSM1429911 SRX647895 GSM1429912 GSM1429912: ESC_H33KD1_nInput; Mus musculus; ChIP-Seq SRP044146 SRS655163 GSM1429912 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 GSM1429912 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429912 gds 301429912 GEO Accession GSM1429912 SRX647896 GSM1429913 GSM1429913: ESC_Control_Input (ctrl for KD1); Mus musculus; ChIP-Seq SRP044146 SRS655164 GSM1429913 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 GSM1429913 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429913 gds 301429913 GEO Accession GSM1429913 SRX647897 GSM1429914 GSM1429914: ESC_H33WT_H3K9me3 (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS655165 GSM1429914 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 GSM1429914 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429914 gds 301429914 GEO Accession GSM1429914 SRX647898 GSM1429915 GSM1429915: ESC_H33KO1_H3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS655166 GSM1429915 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 GSM1429915 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429915 gds 301429915 GEO Accession GSM1429915 SRX647899 GSM1429916 GSM1429916: ESC_H33KO2_H3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS655167 GSM1429916 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 GSM1429916 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429916 gds 301429916 GEO Accession GSM1429916 SRX647900 GSM1429917 GSM1429917: ESC_H33WT_H3 (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS655168 GSM1429917 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 GSM1429917 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429917 gds 301429917 GEO Accession GSM1429917 SRX647901 GSM1429918 GSM1429918: ESC_H33KO1_H3; Mus musculus; ChIP-Seq SRP044146 SRS655169 GSM1429918 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 GSM1429918 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429918 gds 301429918 GEO Accession GSM1429918 SRX647902 GSM1429919 GSM1429919: ESC_H33KO2_H3; Mus musculus; ChIP-Seq SRP044146 SRS655170 GSM1429919 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 GSM1429919 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429919 gds 301429919 GEO Accession GSM1429919 SRX647903 GSM1429920 GSM1429920: ESC_H33WT_DAXX (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS655171 GSM1429920 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 GSM1429920 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429920 gds 301429920 GEO Accession GSM1429920 SRX647904 GSM1429921 GSM1429921: ESC_H33KO1_DAXX; Mus musculus; ChIP-Seq SRP044146 SRS655172 GSM1429921 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 GSM1429921 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429921 gds 301429921 GEO Accession GSM1429921 SRX647905 GSM1429922 GSM1429922: ESC_H33KO2_DAXX; Mus musculus; ChIP-Seq SRP044146 SRS655173 GSM1429922 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 GSM1429922 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429922 gds 301429922 GEO Accession GSM1429922 SRX647906 GSM1429923 GSM1429923: ESC_H33WT_Input (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS655174 GSM1429923 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 GSM1429923 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429923 gds 301429923 GEO Accession GSM1429923 SRX647907 GSM1429924 GSM1429924: ESC_H33KO1_Input; Mus musculus; ChIP-Seq SRP044146 SRS655175 GSM1429924 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 GSM1429924 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429924 gds 301429924 GEO Accession GSM1429924 SRX647908 GSM1429925 GSM1429925: ESC_H33KO2_Input; Mus musculus; ChIP-Seq SRP044146 SRS655176 GSM1429925 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 GSM1429925 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429925 gds 301429925 GEO Accession GSM1429925 SRX647909 GSM1429926 GSM1429926: ESC_H33KD1-H32-HA (addback); Mus musculus; ChIP-Seq SRP044146 SRS655177 GSM1429926 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 GSM1429926 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429926 gds 301429926 GEO Accession GSM1429926 SRX647910 GSM1429927 GSM1429927: ESC_H33KD1-H33-HA (addback); Mus musculus; ChIP-Seq SRP044146 SRS655178 GSM1429927 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 GSM1429927 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429927 gds 301429927 GEO Accession GSM1429927 SRX647911 GSM1429928 GSM1429928: ESC_DAXXWT_H33-HA (ctrl for DAXXnull); Mus musculus; ChIP-Seq SRP044146 SRS655179 GSM1429928 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 GSM1429928 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429928 gds 301429928 GEO Accession GSM1429928 SRX647912 GSM1429929 GSM1429929: ESC_DAXXnull_H33-HA; Mus musculus; ChIP-Seq SRP044146 SRS655180 GSM1429929 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 GSM1429929 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429929 gds 301429929 GEO Accession GSM1429929 SRX647913 GSM1429930 GSM1429930: ESC_DAXXnull_Input; Mus musculus; ChIP-Seq SRP044146 SRS655181 GSM1429930 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 GSM1429930 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1429930 gds 301429930 GEO Accession GSM1429930 SRX769451 GSM1555211 GSM1555211: ESC_DAXXnull_Input-2; Mus musculus; ChIP-Seq SRP044146 SRS753601 GSM1555211 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 GSM1555211 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1555211 gds 301555211 GEO Accession GSM1555211 SRX1022086 GSM1555116 GSM1555116: ESC_H33WT_H33; Mus musculus; ChIP-Seq SRP044146 SRS932040 GSM1555116 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 301555116 GEO Accession GSM1555116 SRX1022087 GSM1555117 GSM1555117: ESC_H33KO1_H33 (ctrl for H3.3 Ab); Mus musculus; ChIP-Seq SRP044146 SRS932038 GSM1555117 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 301555117 GEO Accession GSM1555117 SRX1022088 GSM1555118 GSM1555118: ESC_H33WT_gDNA (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS932037 GSM1555118 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 301555118 GEO Accession GSM1555118 SRX1022089 GSM1555119 GSM1555119: ESC_H33KO1_gDNA; Mus musculus; ChIP-Seq SRP044146 SRS932036 GSM1555119 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 301555119 GEO Accession GSM1555119 SRX1022090 GSM1555120 GSM1555120: ESC_H33WT_KAP1-1 (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS932034 GSM1555120 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 301555120 GEO Accession GSM1555120 SRX1022091 GSM1555121 GSM1555121: ESC_H33KO1_KAP1-1; Mus musculus; ChIP-Seq SRP044146 SRS932035 GSM1555121 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 301555121 GEO Accession GSM1555121 SRX1022092 GSM1555122 GSM1555122: ESC_H33KO2_KAP1-1; Mus musculus; ChIP-Seq SRP044146 SRS932033 GSM1555122 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 301555122 GEO Accession GSM1555122 SRX1022093 GSM1555123 GSM1555123: ESC_H33WT_KAP1-2 (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS932032 GSM1555123 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 301555123 GEO Accession GSM1555123 SRX1022094 GSM1555124 GSM1555124: ESC_H33KO1_KAP1-2; Mus musculus; ChIP-Seq SRP044146 SRS932030 GSM1555124 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 301555124 GEO Accession GSM1555124 SRX1022095 GSM1555125 GSM1555125: ESC_H33KO2_KAP1-2; Mus musculus; ChIP-Seq SRP044146 SRS932031 GSM1555125 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 301555125 GEO Accession GSM1555125 SRX1022096 GSM1555126 GSM1555126: ESC_H33KO1-H32-HA (addback); Mus musculus; ChIP-Seq SRP044146 SRS753974 GSM1555126 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 301555126 GEO Accession GSM1555126 SRX1022097 GSM1555127 GSM1555127: ESC_H33KO1-H33-HA (addback); Mus musculus; ChIP-Seq SRP044146 SRS932029 GSM1555127 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 301555127 GEO Accession GSM1555127 SRX1022098 GSM1555128 GSM1555128: ESC_H33WT_nInput (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS932028 GSM1555128 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 301555128 GEO Accession GSM1555128 SRX1022099 GSM1555129 GSM1555129: ESC_H33KO1_nInput; Mus musculus; ChIP-Seq SRP044146 SRS932027 GSM1555129 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 301555129 GEO Accession GSM1555129 SRX1022100 GSM1555130 GSM1555130: ESC_H33KO2_nInput; Mus musculus; ChIP-Seq SRP044146 SRS932026 GSM1555130 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 301555130 GEO Accession GSM1555130 SRX1022101 GSM1555131 GSM1555131: ESC_H33WT_nH3K9me3 (ctrl for KO); Mus musculus; ChIP-Seq SRP044146 SRS932024 GSM1555131 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 301555131 GEO Accession GSM1555131 SRX1022102 GSM1555132 GSM1555132: ESC_H33KO1_nH3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS932025 GSM1555132 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 301555132 GEO Accession GSM1555132 SRX1022103 GSM1555133 GSM1555133: ESC_H33KO2_nH3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS932023 GSM1555133 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 301555133 GEO Accession GSM1555133 SRX1022104 GSM1555134 GSM1555134: ESC_DAXXWT_H3K9me3 (ctrl for DAXX KO); Mus musculus; ChIP-Seq SRP044146 SRS932022 GSM1555134 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 301555134 GEO Accession GSM1555134 SRX1022105 GSM1555135 GSM1555135: ESC_DAXXnull_H3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS932021 GSM1555135 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 301555135 GEO Accession GSM1555135 SRX1022106 GSM1555136 GSM1555136: ESC_DAXXWT_Input (ctrl for DAXX KO); Mus musculus; ChIP-Seq SRP044146 SRS932020 GSM1555136 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 301555136 GEO Accession GSM1555136 SRX1022107 GSM1555137 GSM1555137: ESC_ATRXWT_H33 (ctrl for ATRX KO); Mus musculus; ChIP-Seq SRP044146 SRS932018 GSM1555137 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 301555137 GEO Accession GSM1555137 SRX1022108 GSM1555138 GSM1555138: ESC_ATRXnull_H33; Mus musculus; ChIP-Seq SRP044146 SRS932017 GSM1555138 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 301555138 GEO Accession GSM1555138 SRX1022109 GSM1555139 GSM1555139: ESC_ATRXWT-H33BHA_H33 (ctrl for ATRX KO); Mus musculus; ChIP-Seq SRP044146 SRS932015 GSM1555139 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 301555139 GEO Accession GSM1555139 SRX1022110 GSM1555140 GSM1555140: ESC_ATRXnull-H33BHA_H33; Mus musculus; ChIP-Seq SRP044146 SRS932016 GSM1555140 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 301555140 GEO Accession GSM1555140 SRX1022111 GSM1555141 GSM1555141: ESC_ATRXWT-H33BHA_HA (ctrl for ATRX KO); Mus musculus; ChIP-Seq SRP044146 SRS932014 GSM1555141 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 301555141 GEO Accession GSM1555141 SRX1022112 GSM1555142 GSM1555142: ESC_ATRXnull-H33BHA_HA; Mus musculus; ChIP-Seq SRP044146 SRS932013 GSM1555142 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 301555142 GEO Accession GSM1555142 SRX1022113 GSM1555143 GSM1555143: ESC_ATRXWT_H3K9me3 (ctrl for ATRX KO); Mus musculus; ChIP-Seq SRP044146 SRS932012 GSM1555143 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 301555143 GEO Accession GSM1555143 SRX1022114 GSM1555144 GSM1555144: ESC_ATRXnull_H3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS932011 GSM1555144 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 301555144 GEO Accession GSM1555144 SRX1022115 GSM1555145 GSM1555145: ESC_ATRXWT_nInput (ctrl for ATRX KO); Mus musculus; ChIP-Seq SRP044146 SRS932010 GSM1555145 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 301555145 GEO Accession GSM1555145 SRX1022116 GSM1555146 GSM1555146: ESC_ATRXnull_nInput; Mus musculus; ChIP-Seq SRP044146 SRS932009 GSM1555146 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 301555146 GEO Accession GSM1555146 SRX1022117 GSM1555147 GSM1555147: ESC_ATRXWT_Input (ctrl for ATRX KO); Mus musculus; ChIP-Seq SRP044146 SRS932008 GSM1555147 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 301555147 GEO Accession GSM1555147 SRX1022118 GSM1555148 GSM1555148: ESC_ATRXnull_Input; Mus musculus; ChIP-Seq SRP044146 SRS932007 GSM1555148 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 301555148 GEO Accession GSM1555148 SRX1022119 GSM1555149 GSM1555149: ESC_KAP1WT_H33 (ctrl for KAP1 KO); Mus musculus; ChIP-Seq SRP044146 SRS932006 GSM1555149 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 301555149 GEO Accession GSM1555149 SRX1022120 GSM1555150 GSM1555150: ESC_KAP1KO_H33; Mus musculus; ChIP-Seq SRP044146 SRS932005 GSM1555150 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 301555150 GEO Accession GSM1555150 SRX1022121 GSM1555151 GSM1555151: ESC_KAP1WT_Input (ctrl for KAP1 KO); Mus musculus; ChIP-Seq SRP044146 SRS932004 GSM1555151 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 301555151 GEO Accession GSM1555151 SRX1022122 GSM1555152 GSM1555152: ESC_KAP1KO_Input; Mus musculus; ChIP-Seq SRP044146 SRS932003 GSM1555152 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 301555152 GEO Accession GSM1555152 SRX1022123 GSM1555153 GSM1555153: ESC_ESETWT_H33 (ctrl for ESET KO); Mus musculus; ChIP-Seq SRP044146 SRS932002 GSM1555153 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 301555153 GEO Accession GSM1555153 SRX1022124 GSM1555154 GSM1555154: ESC_ESETKO_H33; Mus musculus; ChIP-Seq SRP044146 SRS932001 GSM1555154 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 301555154 GEO Accession GSM1555154 SRX1022125 GSM1555155 GSM1555155: ESC_ESETWT_H33-H3K9me3 (ctrl for ESET KO); Mus musculus; ChIP-Seq SRP044146 SRS932000 GSM1555155 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 301555155 GEO Accession GSM1555155 SRX1022126 GSM1555156 GSM1555156: ESC_ESETKO_H33-H3K9me3; Mus musculus; ChIP-Seq SRP044146 SRS931999 GSM1555156 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 301555156 GEO Accession GSM1555156 SRX1022127 GSM1555157 GSM1555157: ESC_ESETWT_Input (ctrl for ESET KO); Mus musculus; ChIP-Seq SRP044146 SRS931997 GSM1555157 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 301555157 GEO Accession GSM1555157 SRX1022128 GSM1555158 GSM1555158: ESC_ESETKO_Input; Mus musculus; ChIP-Seq SRP044146 SRS932019 GSM1555158 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 301555158 GEO Accession GSM1555158