GSM5288697: 4T1 cells, 11A_KD_CHD8_IP (ChIPseq); Mus musculus; ChIP-Seq
ChIP-Seq experiments were performed as described (Schmidt et al Methods 2009). Antibodies used were BCL11A (Bethyl, A300-382A and Abcam ab191401) and CHD8 (Novus NB100-60417 and Bethyl A301-225A-M). Briefly 2 × 15 cm plates per cell line were formaldehyde crosslinked, nuclear fraction was isolated and chromatin sonicated using Bioruptor Pico (Diagenode). IP was performed using 100 μl of Dynabeads Protein G (Thermo Fisher Scientific) and 10 μg of antibody. The samples were then reverse crosslinked and DNA was eluted using Qiagen MinElute column. Samples were then processed for library prep and sequencing. ChIP-Seq libraries were prepared using the ThruPLEX DNA-seq Kit. The pool was run as a PE150 run type on one lane of a HiSeq 4000. ChIPseq, PE150