Wrab 1200

Snap-frozen mouse or human liver (100 mg) was used to prepare chromatin. ChIP and ChIP-seq were performed as reported previously (Kain et al. 2021 (link)). Briefly, liver tissue was minced in cold PBS and cross-linked in 1% formaldehyde/PBS for 15 min with constant rotation in a Labquake tube rotator. Cross-linking was quenched by adding glycine to a final concentration of 0.125 M. Nuclear lysate was sonicated using a Diagenode Bioruptor Pico for 14 cycles (30 sec on/30 sec off). FOXA2-specific rabbit antiserum (Seven Hills Bioreagents WRAB-1200), rabbit antibody to lamin B1 (Abcam Ab16048), and anti-Histone H3 (trimethyl K9) rabbit antibody (ab8898) were used for immunoprecipitation. Libraries were made according to standard Illumina protocol (end-repair of ChIP DNA, addition of A base to the 3′-ends, adapter ligation, and amplification). We used multiplex adapters for sequencing and Kapa HiFi DNA polymerase (Kapa Biosystems) for PCR amplification (16 cycles). Library fragments were isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 and NextSeq 2000 instruments following the manufacturer's protocols.