FASTQ files of sequencing reads were retrieved from the sequencing machine and the sequences were aligned using Bowtie algorithm for identifying uniquely mapping region allowing for a maximum of 2 mismatches
We have performed short DNA sequencing protocol per instructions from the manufacturere (Illumina). 35 bases were sequenced.
MCF10A cells were cultured with DMEM/F12 media supplemented with 2.5% Horse serum, 0.5ug/mL hydrocortisone, 10ug/mL Insulin, 20ng/mL EGF and 100ng/mL cholera toxin. IMR90 cells were cultured in MEM with Earles salts with 10% FBS.
We have followed the ChIP protocol previously published in Kim, T.H. et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128, 17382889 (2007). The ChIP DNA was further processed by the Yale Center for Genomic Analysis following the instructions from Illumina, Inc. 35 bases were sequenced.