Chromatin Immunoprecipitation and Sequencing

Hundred to two hudredred milligrams of flash-frozen liver tissue was homogenized with a tissue Dounce as previously described and subsequent micrococcal digest, chromatin immunoprecipitation, and library preparation were carried out as described^{2 (link)}. The antibodies used for ChIPseq and the concentrations, volumes and sources are anti-H3K4me3 (Abcam, ab1012 1 µg/µl; used 6 µl), anti-H3K27me3 (Active Motif, 61017; 1 µg/µl; used 6 µl), anti-H3K9me3 (Active Motif, 39161; 1 µg/µl; used 6 µl), and anti-H2AZ (Abcam, ab4174; 1 µg/µl; used 10 µl). The prepared libraries were sequenced on the Hiseq2500 platform for 75 bp single-end or 100 bp paired-end reads read runs at the Core Technology Platforms (CTP) at New York University Abu Dhabi (NYUAD). After sequencing, 75 base-pair single-end or 100 base-pair paired-end reads that passed quality trimming were aligned against the mouse reference genome (GRCm38.p4) using BWA-MEM^{77 (link)}. The resulting BAM files were then processed through PICARD tools (to clean, deduplicate and sort) for downstream analysis and visualization. One sample from each timepoint and antibody was used.