Reanalysis of white and brite adipocyte ChIP-Seq of PPARG and MED1 in the hg38 genome

To compare the binding of PPARG and MED1 at the TSSes of differentially expressed isoforms in white and brite (also known as beige) adipocytes, data from GSE59703 (Loft et al., 2015) was reanalysed on the hg38 genome. We find that a large majority of the splice variants arise from differential TSS usage, with beige-specific TSSs being enriched for PPARγ and MED1 binding compared to white-specific TSSs. PPARgamma, MED1 ChIP-Seq and Input reads for white and brite adipocytes were downloaded from Gene Expression Omnibus (GEO) accession GSE59703 (Loft et al. 2015). These consisted of two replicates per antibody in each condition and an input file per condition to a total of 10 samples. Reads from replicates were merged and aligned to hg38 using Bowtie2. Peaks were detected using MACS3. ChIP/Input ratio tracks were generated using bamCompare in deepTools. Mean ratios (ChIP/Input) of the PPARgamma and MED1 were calculated for +/- 250 bp windows around the TSS using multiBigwigSummary from deepTools.