title: GSM5508187: TCF3-ZNF384 -e8 HA Replicate 3; Mus musculus; ChIP-Seq
library_construction_protocol: Chromatin was prepared as described (Zhang et.al, Nature Genetics, 2016). Breifly, 20 X 10^6 cells were crosslinked with 1% formaldehyde for 10 minutes. Cells were washed 3 times with PBS and lysed on ice for 10 minutes with lysis buffer. Chromatin was washed twice in wash buffer and once in shearing buffer before resuspending in 1ml of shearing buffer. Chromatin was sonicated with a Covaris E210 instrument and resuspended in dilution buffer. Finally, immunoprecipiation was performed with anti-HA antibody. Chipmentation was performed as described () on 1-2 x 10^6 cells. To prepare ChIP–seq libraries, 10 ng of ChIP DNA was end repaired and adaptor ligation was performed using the NEBNext ChIP–Seq Library Prep Reagent Set for Illumina (New England BioLabs). Libraries were purified after 14 rounds of PCR amplification with Q5 DNA Hot-Start polymerase (New England BioLabs). Each ChIP–seq library underwent 50-cycle single-end sequencing using TruSeq SBS kit v3 on an Illumina HiSeq 2000. ChIPmentation libraries were prepared using Kapa HiFi HotStart ReadyMix and Nextera primers. The libraries were sequenced using the Illumina HiSeq3000/4000 platform and the 25 base pair, paired-end configuration.