, ChIP samples were prepared as described previously 21 , with minor modifications. Briefly, fresh livers were chopped into small pieces and crosslinked with 1% formaldehyde (ThermoFisher, 28906) in PBS for 10 min for histone modifications, or double crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min, for TFs and GPS2. The reaction was stopped with glycine at a final concentration of 0.125 M for 5 min
, Dounce Homogenizer first with loose and later with tight pestle (Fisher Science, FB56691)
, Formaldehyde cross-linking was reversed overnight at 65°C, and the immunoprecipitated DNA was purified using the QIAquick PCR purification kit (Qiagen). Primers for the ChIP qPCR are listed in Supplementary Table 1. To prepare the ChIP-seq samples, the same ChIP protocol was followed, but using the ChIP DNA Clean and Concentrator Capped Zymo-Spin I (Zymo Research) purification kit. Two to four ChIPs were pooled during the final step of the purification to obtain concentrated material. For library preparation and sequencing, 2-10 ng of ChIPed DNA was processed using Rubicon ThruPLEX DNA-seq kit (TAKARA) or processed at the EMBL Genomics Core Facility, sc-2027, 1-5 ?g), anti-H3K4me3 (Abcam, ab8580, 1 ?g), anti-H3K27ac (Abcam, ab4729, 1 ?g), anti-PPAR? (Millipore MAB3890, 5 ?g), anti-Polymerase II (Biolegend, 664906, 5 ?g), anti-NCOR (Bethyl laboratories, A301-145A, 4 ?g), anti-SMRT (Bethyl laboratories, A301-147A, 4 ?g)
, The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under Project SNIC 2018/8-122. Analysis was performed as previously described 21 . Sequencing files (fastq files), provided by the EMBL, Genomics
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