ChIP-seq of RNA polymerase II and HNF4alpha in mouse liver after cytokine stimulation (WT vs TG)

ChIP-seq was performed on liver samples from 6-week-old male mice (WT and TG) following a single intravenous injection of mouse TNFalpha (BioLegend, 7.5 ug/kg) or vehicle. Livers were collected 4 h post-injection. ChIP was carried out using anti-RNA polymerase II (Active Motif) or anti-HNF4alpha (Abcam) with matched input controls. Single-end reads were sequenced on an Illumina HiSeq 2000 platform, aligned to the mouse reference genome (mm10) using Bowtie, and peaks were called using MACS2 (v2.0.10.20120913) with matched input controls.