Sheet1 Data GEO ID Type Reference Column1 Column2 Column3 Column4 Column5 Column6 Column7 Column8 Column9 Column10 Column11 Column12 Column13 Column14 Column15 Column16 Column17 Column18 Column19 Column20 Column21 Column22 Column23 Column24 Column25 Column26 Column27 Column28 Column29 Column30 Column31 Column32 Column33 Column34 Column35 Column36 Column37 Column38 Column39 Column40 Column41 Column42 Column43 Column44 Column45 Column46 Column47 Column48 Column49 Column50 Column51 Column52 Column53 Column54 Column55 Column56 Column57 Column58 Column59 Column60 Column61 Column62 Column63 Column64 Column65 Column66 Column67 Column68 Column69 Column70 Column71 Column72 Column73 Column74 Column75 Column76 Column77 Column78 Column79 Column80 Column81 Column82 Column83 Column84 Column85 Column86 Column87 Column88 Column89 Column90 Column91 Column92 Column93 Column94 Column95 Column96 Column97 Column98 Column99 Column100 Column101 Column102 Column103 Column104 Column105 Column106 Column107 Column108 Column109 Column110 Column111 Column112 Column113 Column114 Column115 Column116 Column117 Column118 Column119 Column120 Column121 Column122 Column123 Column124 Column125 Column126 Column127 Column128 Column129 Column130 Column131 Column132 Column133 Column134 Column135 Column136 Column137 Column138 Column139 Column140 Column141 Column142 Column143 Column144 Column145 Column146 Column147 Column148 Column149 Column150 Column151 Column152 Column153 Column154 Column155 Column156 Column157 Column158 Column159 Column160 Column161 Column162 Column163 Column164 Column165 Column166 Column167 Column168 Column169 Column170 Column171 Column172 Column173 Column174 Column175 Column176 Column177 Column178 Column179 Column180 Column181 Column182 Column183 Column184 Column185 Column186 Column187 Column188 Column189 Column190 Column191 Column192 Column193 Column194 Column195 Column196 Column197 Column198 Column199 Column200 Column201 Column202 Column203 Column204 Column205 Column206 Column207 Column208 Column209 Column210 Column211 Column212 Column213 Column214 Column215 Column216 Column217 Column218 Column219 Column220 Column221 Column222 Column223 Column224 Column225 Column226 Column227 Column228 Column229 Column230 Column231 Column232 Column233 Column234 Column235 Column236 Column237 Column238 Column239 Column240 Column241 Column242 Column243 Column244 Column245 Column246 Column247 Column248 Column249 Column250 Column251 Column252 H3K4me1 GSE11172 ChIP-Seq Meissner A, Mikkelsen TS, Gu H, Wernig M et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008 Aug 7;454(7205):766-70 H3K4me2 GSE11172 ChIP-Seq Meissner A, Mikkelsen TS, Gu H, Wernig M et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008 Aug 7;454(7205):766-70 C_MYC GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 CTCF GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 E2F1 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 P300 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 ESRRB GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 KLF4 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 N_MYC GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 NANOG GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 OCT4 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 SMAD1 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 SOX2 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 STAT3 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 SUZ12 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 TCFCP2L1 GSE11431 ChIP-Seq Chen X, Xu H, Yuan P, Fang F et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008 Jun 13;133(6):1106-17 DNA control GSE11724 DNA Input Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. H3K36me3 GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. H3K4me3 GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. H3K79me2 GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. NANOG GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. OCT4 GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. SOX2 GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. SUZ12 GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. TCF3 GSE11724 ChIP-Seq Marson A, Levine SS, Cole MF, Frampton GM et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008 Aug 8;134(3):521-33. DNA control GSE12241 DNA Input Mikkelsen TS, Ku M, Jaffe DB, Issac B et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2;448(7153):553-60. H3K27me3 GSE12241 ChIP-Seq Mikkelsen TS, Ku M, Jaffe DB, Issac B et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2;448(7153):553-60. H3K36me3 GSE12241 ChIP-Seq Mikkelsen TS, Ku M, Jaffe DB, Issac B et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2;448(7153):553-60. H3K4me3 GSE12241 ChIP-Seq Mikkelsen TS, Ku M, Jaffe DB, Issac B et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2;448(7153):553-60. H3K9me3 GSE12241 ChIP-Seq Mikkelsen TS, Ku M, Jaffe DB, Issac B et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2;448(7153):553-60. H4K20me3 GSE12241 ChIP-Seq Mikkelsen TS, Ku M, Jaffe DB, Issac B et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2;448(7153):553-60. RPOLII GSE12241 ChIP-Seq Mikkelsen TS, Ku M, Jaffe DB, Issac B et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007 Aug 2;448(7153):553-60. BRG1 GSE14344 ChIP-Seq Ho L, Jothi R, Ronan JL, Cui K et al. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci U S A 2009 Mar 31;106(13):5187-91. DNA control GSE14344 IgG input Ho L, Jothi R, Ronan JL, Cui K et al. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci U S A 2009 Mar 31;106(13):5187-91. DNA control GSE18371 DNA Input Bilodeau S, Kagey MH, Frampton GM, Rahl PB et al. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 2009 Nov 1;23(21):2484-9. H3K9me3 GSE18371 ChIP-Seq Bilodeau S, Kagey MH, Frampton GM, Rahl PB et al. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 2009 Nov 1;23(21):2484-9. SETDB1 GSE18371 ChIP-Seq Bilodeau S, Kagey MH, Frampton GM, Rahl PB et al. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 2009 Nov 1;23(21):2484-9. LSD1 GSE18515 ChIP-Seq Nair VD, Ge Y, Balasubramaniyan N, Kim J et al. Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells. Mol Cell Biol 2012 Dec;32(23):4861-76. DNA control GSE18515 DNA Input Nair VD, Ge Y, Balasubramaniyan N, Kim J et al. Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells. Mol Cell Biol 2012 Dec;32(23):4861-76. DNA control GSE22562 DNA Input Kagey MH, Newman JJ, Bilodeau S, Zhan Y et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010 Sep 23;467(7314):430-5 MED12 GSE22562 ChIP-Seq Kagey MH, Newman JJ, Bilodeau S, Zhan Y et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010 Sep 23;467(7314):430-5 MED1 GSE22562 ChIP-Seq Kagey MH, Newman JJ, Bilodeau S, Zhan Y et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010 Sep 23;467(7314):430-5 NIPBL GSE22562 ChIP-Seq Kagey MH, Newman JJ, Bilodeau S, Zhan Y et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010 Sep 23;467(7314):430-5 SMC1 GSE22562 ChIP-Seq Kagey MH, Newman JJ, Bilodeau S, Zhan Y et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010 Sep 23;467(7314):430-5 SMC3 GSE22562 ChIP-Seq Kagey MH, Newman JJ, Bilodeau S, Zhan Y et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010 Sep 23;467(7314):430-5 CTCF GSE24030 ChIP-Seq Nitzsche A, Paszkowski-Rogacz M, Matarese F, Janssen-Megens EM et al. RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS One 2011 May 12;6(5):e19470. DNA control GSE24030 IgG input Nitzsche A, Paszkowski-Rogacz M, Matarese F, Janssen-Megens EM et al. RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS One 2011 May 12;6(5):e19470. RAD21 GSE24030 ChIP-Seq Nitzsche A, Paszkowski-Rogacz M, Matarese F, Janssen-Megens EM et al. RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PLoS One 2011 May 12;6(5):e19470. DNA control GSE24843 IgG input Williams K, Christensen J, Pedersen MT, Johansen JV et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011 May 19;473(7347):343-8 SIN3A GSE24843 ChIP-Seq Williams K, Christensen J, Pedersen MT, Johansen JV et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011 May 19;473(7347):343-8 TET1 GSE24843 ChIP-Seq Williams K, Christensen J, Pedersen MT, Johansen JV et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011 May 19;473(7347):343-8 DNA control GSE27841 DNA Input Whyte WA, Bilodeau S, Orlando DA, Hoke HA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012 Feb 1;482(7384):221-5. HDAC1 GSE27841 ChIP-Seq Whyte WA, Bilodeau S, Orlando DA, Hoke HA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012 Feb 1;482(7384):221-5. HDAC2 GSE27841 ChIP-Seq Whyte WA, Bilodeau S, Orlando DA, Hoke HA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012 Feb 1;482(7384):221-5. LSD1 GSE27841 ChIP-Seq Whyte WA, Bilodeau S, Orlando DA, Hoke HA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012 Feb 1;482(7384):221-5. MI2B GSE27841 ChIP-Seq Whyte WA, Bilodeau S, Orlando DA, Hoke HA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012 Feb 1;482(7384):221-5. REST GSE27841 ChIP-Seq Whyte WA, Bilodeau S, Orlando DA, Hoke HA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012 Feb 1;482(7384):221-5. CoREST GSE27841 ChIP-Seq Whyte WA, Bilodeau S, Orlando DA, Hoke HA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 2012 Feb 1;482(7384):221-5. CTCF GSE28247 ChIP-Seq Handoko L, Xu H, Li G, Ngan CY et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011 Jun 19;43(7):630-8. DNA control GSE28247 DNA Input Handoko L, Xu H, Li G, Ngan CY et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011 Jun 19;43(7):630-8. EP300 GSE28247 ChIP-Seq Handoko L, Xu H, Li G, Ngan CY et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011 Jun 19;43(7):630-8. LaminB GSE28247 ChIP-Seq Handoko L, Xu H, Li G, Ngan CY et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011 Jun 19;43(7):630-8. RPOLII GSE28247 ChIP-Seq Handoko L, Xu H, Li G, Ngan CY et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011 Jun 19;43(7):630-8. 5hmC GSE28682 GLIB method Pastor WA, Pape UJ, Huang Y, Henderson HR et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011 May 19;473(7347):394-7. 5mC GSE28682 MeDIP-Seq Pastor WA, Pape UJ, Huang Y, Henderson HR et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011 May 19;473(7347):394-7. DNA control GSE28682 negative GLIB Pastor WA, Pape UJ, Huang Y, Henderson HR et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011 May 19;473(7347):394-7. H3K27ac GSE31039-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. H3K36me3 GSE31039-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. H3K4me1 GSE31039-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. H3K4me3 GSE31039-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. H3K9ac GSE31039-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. DNA control GSE32218-ENCODE DNA Input ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. H3K4me3 GSE32218-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. H3K9me3 GSE32218-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. DNA control GSE34518 MockIP Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. H2Aub1 GSE34518 ChIP-Seq Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. H3K36me3 GSE34518 ChIP-Seq Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. RING1B GSE34518 ChIP-Seq Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. RNAPII_8WG16 GSE34518 ChIP-Seq Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. RNAPII_S2P GSE34518 ChIP-Seq Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. RNAPII_S5P GSE34518 ChIP-Seq Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. RNAPII_S7P GSE34518 ChIP-Seq Brookes E, de Santiago I, Hebenstreit D, Morris KJ et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 2012 Feb 3;10(2):157-70. DNA control GSE36030-ENCODE DNA Input ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. HCFC1 GSE36030-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. MAFK GSE36030-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. ZC3H11A GSE36030-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. ZNF384 GSE36030-ENCODE ChIP-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. DNA control GSE36114 IgG input Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. H2AZ GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. H3K27ac GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. H3K27me3 GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. H3K36me3 GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. H3K4me1 GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. H3K4me2 GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. H3K4me3 GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. TAF1 GSE36114 ChIP-Seq Xiao S, Xie D, Cao X, Yu P et al. Comparative epigenomic annotation of regulatory DNA. Cell 2012 Jun 8;149(6):1381-92. DNAseI GSE37074-ENCODE DNAseI-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. DNA control GSE39154 IgG input Vella P, Scelfo A, Jammula S, Chiacchiera F et al. Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. Mol Cell 2013 Feb 21;49(4):645-56 OGT GSE39154 ChIP-Seq Vella P, Scelfo A, Jammula S, Chiacchiera F et al. Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. Mol Cell 2013 Feb 21;49(4):645-56 DNA control GSE39610 DNA Input Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. MBD1a GSE39610 ChIP-Seq Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. MBD1b GSE39610 ChIP-Seq Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. MBD2a GSE39610 ChIP-Seq Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. MBD2T GSE39610 ChIP-Seq Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. MBD3a GSE39610 ChIP-Seq Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. MBD4 GSE39610 ChIP-Seq Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. MeCP2 GSE39610 ChIP-Seq Baubec T, Ivánek R, Lienert F, Schübeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013 Apr 11;153(2):480-92. RNA GSE39619-ENCODE RNA-Seq ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 Sep 6;489(7414):57-74. 5fC GSE40148 Raiber EA, Beraldi D, Ficz G, Burgess HE et al. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol 2012 Aug 17;13(8):R69. DNA control GSE40148 DNA Input Raiber EA, Beraldi D, Ficz G, Burgess HE et al. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biol 2012 Aug 17;13(8):R69. KDM2A GSE40860 ChIP-Seq Farcas AM, Blackledge NP, Sudbery I, Long HK et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife (Cambridge) 2012 Dec 18;1:e00205. KDM2B GSE40860 ChIP-Seq Farcas AM, Blackledge NP, Sudbery I, Long HK et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife (Cambridge) 2012 Dec 18;1:e00205. DNA control GSE40860 DNA Input Farcas AM, Blackledge NP, Sudbery I, Long HK et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife (Cambridge) 2012 Dec 18;1:e00205. DNA control GSE41589 IgG input Ballaré C, Lange M, Lapinaite A, Martin GM et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012 Dec;19(12):1257-65 DNA control GSE41589 IgG(Hi) input Ballaré C, Lange M, Lapinaite A, Martin GM et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012 Dec;19(12):1257-65 H3K27me3 GSE41589 ChIP-Seq Ballaré C, Lange M, Lapinaite A, Martin GM et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012 Dec;19(12):1257-65 H3K36me2 GSE41589 ChIP-Seq Ballaré C, Lange M, Lapinaite A, Martin GM et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012 Dec;19(12):1257-65 H3K36me3 GSE41589 ChIP-Seq Ballaré C, Lange M, Lapinaite A, Martin GM et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012 Dec;19(12):1257-65 PHF19 GSE41589 ChIP-Seq Ballaré C, Lange M, Lapinaite A, Martin GM et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012 Dec;19(12):1257-65 SUZ12 GSE41589 ChIP-Seq Ballaré C, Lange M, Lapinaite A, Martin GM et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol 2012 Dec;19(12):1257-65 DNA control GSE41609 DNA Input Brien GL, Gambero G, O'Connell DJ, Jerman E et al. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. Nat Struct Mol Biol 2012 Dec;19(12):1273-81. PHF19 GSE41609 ChIP-Seq Brien GL, Gambero G, O'Connell DJ, Jerman E et al. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. Nat Struct Mol Biol 2012 Dec;19(12):1273-81. KAP1 GSE41903 ChIP-Seq Rowe HM, Kapopoulou A, Corsinotti A, Fasching L et al. TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res 2013 Mar;23(3):452-61. DNA control GSE41903 DNA Input Rowe HM, Kapopoulou A, Corsinotti A, Fasching L et al. TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res 2013 Mar;23(3):452-61. CBX7 GSE42466 ChIP-Seq Morey L, Aloia L, Cozzuto L, Benitah SA et al. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Cell Rep 2013 Jan 31;3(1):60-9. DNA control GSE42466 IgG_old input Morey L, Aloia L, Cozzuto L, Benitah SA et al. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Cell Rep 2013 Jan 31;3(1):60-9. DNA control GSE42466 IgG input Morey L, Aloia L, Cozzuto L, Benitah SA et al. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Cell Rep 2013 Jan 31;3(1):60-9. RING1B GSE42466 ChIP-Seq Morey L, Aloia L, Cozzuto L, Benitah SA et al. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Cell Rep 2013 Jan 31;3(1):60-9. RYBP GSE42466 ChIP-Seq Morey L, Aloia L, Cozzuto L, Benitah SA et al. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Cell Rep 2013 Jan 31;3(1):60-9. SUZ12 GSE42466 ChIP-Seq Morey L, Aloia L, Cozzuto L, Benitah SA et al. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Cell Rep 2013 Jan 31;3(1):60-9. CBX3 GSE44242 ChIP-Seq Sridharan R, Gonzales-Cope M, Chronis C, Bonora G et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat Cell Biol 2013 Jul;15(7):872-82. DNA control GSE44242 DNA Input Sridharan R, Gonzales-Cope M, Chronis C, Bonora G et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat Cell Biol 2013 Jul;15(7):872-82. DNA control GSE46536 DNA Input Mozzetta C, Pontis J, Fritsch L, Robin P et al. The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing. Mol Cell 2014 Jan 23;53(2):277-89 EZH2 GSE46536 ChIP-Seq Mozzetta C, Pontis J, Fritsch L, Robin P et al. The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing. Mol Cell 2014 Jan 23;53(2):277-89 G9A GSE46536 ChIP-Seq Mozzetta C, Pontis J, Fritsch L, Robin P et al. The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing. Mol Cell 2014 Jan 23;53(2):277-89 DNA control GSE48172 DNA Input Hu D, Garruss AS, Gao X, Morgan MA et al. The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells. Nat Struct Mol Biol 2013 Sep;20(9):1093-7 MLL2 GSE48172 ChIP-Seq Hu D, Garruss AS, Gao X, Morgan MA et al. The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells. Nat Struct Mol Biol 2013 Sep;20(9):1093-7 DNA control GSE48175 IgG input Krepelova A, Neri F, Maldotti M, Rapelli S et al. Myc and max genome-wide binding sites analysis links the Myc regulatory network with the polycomb and the core pluripotency networks in mouse embryonic stem cells. PLoS One 2014;9(2):e88933. MAX GSE48175 ChIP-Seq Krepelova A, Neri F, Maldotti M, Rapelli S et al. Myc and max genome-wide binding sites analysis links the Myc regulatory network with the polycomb and the core pluripotency networks in mouse embryonic stem cells. PLoS One 2014;9(2):e88933. LaminB1 UCSC DamID technique Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SWM, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M et al. Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation. Molecular Cell. 2010 May 28;38(4):603-13 5hmC ESC GSE40810 hMeDIP-Seq Tan L, Xiong L, Xu W, Wu F et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res 2013 Apr;41(7):e84 5hmC NPC GSE40810 hMeDIP-Seq Tan L, Xiong L, Xu W, Wu F et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res 2013 Apr;41(7):e84 DNA control ESC GSE40810 DNA Input Tan L, Xiong L, Xu W, Wu F et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res 2013 Apr;41(7):e84 DNA control NPC GSE40810 DNA Input Tan L, Xiong L, Xu W, Wu F et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res 2013 Apr;41(7):e84 ChIA-PET Supplementary Table 2 ChIA-PET Zhang Y, Wong CH, Birnbaum RY, Li G et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 2013 Dec 12;504(7479):306-10 CAGE Supplementary Data Set 2 CAGE Fort A, Hashimoto K, Yamada D, Salimullah M, et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet. 2014 Jun;46(6):558-66 &C&"Times New Roman,Regular"&12&A &C&"Times New Roman,Regular"&12Page &P Sheet2 &C&"Times New Roman,Regular"&12&A &C&"Times New Roman,Regular"&12Page &P Sheet3 &C&"Times New Roman,Regular"&12&A &C&"Times New Roman,Regular"&12Page &P