ChIP-seq protocol for liver tissue

The ChIP-seq protocol used was as described by Schmidt et al.^{68 (link)} Briefly, livers were isolated from 10 to 12 weeks old mice and liver tissue was post mortem cross-linked using 1% formaldehyde (v/v), lysed and sonicated. Protein-bound DNA was immunoprecipitated using 10 µg of an antibody against CEBPA (Santa Cruz, sc-9314), HNF4A (ARP 31946_P050), FOXA1 (ab5089, Abcam), H3K27ac (ab4729, Abcam), or H3K4me3 (Millipore 05-1339). Immunoprecipitated DNA was end-repaired at 20 °C for 30 min, Adenine overhang was added at 37 °C for 30 min, and Illumina sequencing adapters ligated at room temperature for 15 min before 16 cycles of PCR amplification. PCR conditions: (1) 98 °C—30 s; (2) 98 °C—30 s, 65 °C—30 s, 72 °C—30 s, 16 cycles; (3) 72 °C—5 min. DNA fragments ranging from 200- to 300-bp in size were selected on a 2% agarose gel for 50-bp single-end read sequencing on an Illumina HiSeq 2000 according to the manufacturer’s instructions.