title: ChIP-Seq of Mus musculus: wt
design: Freshly dissected liver samples (about one gram) were grinded with razor, homogenized in Dounce homogenizer in 1 ml of 3% formaldehyde, then samples were transferred in 50 ml tube and volume of 3% was adjusted to 40 ml. After 10 min incubation at RT the fixator was quenched by addition of glycine to 125 mM final, incubated 10 min and washed twice by ice-cold PBS, then snap-freezed and stored at -80C. Frozen samples were thawed and lysed for 30minutes in a lysis buffer (10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, protease inhibitors) supplemented with  0.5% SDS. Chromatin was shared using a Bandelin Sonopulse sonicator (70% power within 11 cycles of 30/90sec ON/OFF). 20-40 g of fixed chromatin were used per one ChIP. Before incubation with specific antibodies, chromatin was diluted with a lysis buffer up to 0.1-0.2% SDS and pre-cleared by incubation with Protein A magnetic beads (New England Biolabs, S1425S) for 2h at 4C with slow rotation. During this time, another aliquot of Protein A magnetic beads was washed in PBS, combined with 5 g target antibodies, and incubated for 2h at 4C with slow rotation. Beads were removed and pre-cleared chromatin was immunoprecipitated with antibody/magnetic beads complexes and incubated overnight at 4C with slow rotation. Next day, the beads were thoroughly washed in a series of buffers (Buffer 1: 10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, protease inhibitors; Buffer 2: 500 mM NaCl, 10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, protease inhibitors; Buffer 3: 0.25 M LiCl, 10 mM Tris-HCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate; Buffer TE/Triton: 10 mM Tris-HCl, 1 mM EDTA, 1% Triton X-100; TE buffer: 10 mM Tris-HCl, 1 mM EDTA). Cross-links were removed and DNA was eluted in 100 L elution buffer (10 mM Tris-HCl, 1 mM EDTA, 1% SDS) by incubation at 65C for 14 hours. After treatment with RNAse A (New England Biolabs, T3018) and Proteinase K (New England Biolabs, P8107S), magnetic beads were removed. DNA was extracted using ChIP DNA Clean & Concentrator columns (Zymo Research, D5205). ChIP-seq libraries were prepared for sequencing using Kapa Hyper Prep Kit (Roche, #KK8504) and a KAPA Single-Indexed Adapter Set A, (Roche, #KK8701). Libraries were sequenced on DNBSEQ sequencing platform. ChIP-Seq data were processed by the standard ENCODE pipeline (https://github.com/kundajelab/chipseq_pipeline).