SRX2874158 GSM2645440 SRP108381 SRS2244239 GSM2645440 OTHER GENOMIC other Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 300-700 bp were immunoprecipitated using YY1 or CTCF antibody. Immunoprecipitated DNA was end-repaired, A-tailed, and proximity ligation was performed in the presence of a bridge-linker (5'-ACGCGATATCTTATCTGACT) with T4 DNA ligase. Unligated DNA was digested with exonuclease treatment followed by RNAse A, and Proteinase K treatment. DNA was then phenol:chloroform:isoamyl alcohol preciptated and subjected to library preperation. Purified immunoprecipitated DNA were prepared for sequencing according to the Illumina Nextera Tagmentation protocol. Tagmented DNA was subjected to 12 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 300 and 500bp (representing shear fragments between 200 and 400 nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Illumina HiSeq 2500 gds 302645440 GSM2645440 GEO Accession GSM2645440 SRX2874159 GSM2645441 SRP108381 SRS2244240 GSM2645441 OTHER GENOMIC other Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 300-700 bp were immunoprecipitated using YY1 or CTCF antibody. Immunoprecipitated DNA was end-repaired, A-tailed, and proximity ligation was performed in the presence of a bridge-linker (5'-ACGCGATATCTTATCTGACT) with T4 DNA ligase. Unligated DNA was digested with exonuclease treatment followed by RNAse A, and Proteinase K treatment. DNA was then phenol:chloroform:isoamyl alcohol preciptated and subjected to library preperation. Purified immunoprecipitated DNA were prepared for sequencing according to the Illumina Nextera Tagmentation protocol. Tagmented DNA was subjected to 12 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 300 and 500bp (representing shear fragments between 200 and 400 nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Illumina HiSeq 2500 gds 302645441 GSM2645441 GEO Accession GSM2645441