GSM2575047: HuDEP-6-IN_S3_L003; Homo sapiens; ChIP-Seq
ChIP experiments were performed as previously described (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using highthroughput  sequencing to discover protein-DNA interactions. Methods. Jul 2009;48(3):240-248). Approximately 5 x 107 cells were used for each IP. ChIP-Seq experiments were conducted on two replicates of K1ER cells induced with 200 nM Tamoxifen for 2 hrs, and two replicates of HUDEP-2 cells. The antibodies  used  were  α-KLF1  (PIEPA5-18031,  Thermo  Scientific),  anti-goat  IgG  (SCZSC-2028,  Santa Cruz) as a negative control. Library  preparation  was  performed  using  the  TruSeq  DNA  Sample  Preparation  Kit  (FC-121-2001, Illumina) according to the manufacturer’s instructions with minor modifications. Adapter sequences were diluted 1/40 before use and following adapter ligation, the library size extracted from the gel was 100-280 bp (excluding adapters) in line with the size of sonicated fragments. Libraries (2 inputs and 2 IP samples) were multiplexed into 2 lanes such that there were 2 samples per lane. Samples were  sequenced  using  50  bp  single  read  chemistry  on  the  HiSeq  2500  (Illumina).