ChIPseq in 159 DNMT TKO mESCs upon p300 inhibition
To test if H3K27Ac contributes to chromatin accessibility at enhancers, we globally reduced H3K27Ac levels by chemical inhibition of the histone acetylase p300 (with the small molecule A-485, final concentration 3 µM). This dataset includes ChIP-seq data for H3K27Ac with spike-in normalization, comparing DMSO and A-485 treated samples in mouse cells (i.e., XY 159 knock-out of the three DNA methyl transferases (DNMT TKO) mESCs). Two biological replicates were generated for each treatment condition. In summary, after treating the cells for 24h, cross-link ChIP-seq was performed. The protocol was adapted from (Trovato et al., 2024), with minor modifications. Chromatin was sheared using the Bioruptor Pico (Diagenode) and incubated with the antibody against H3K27ac (ab4729, Abcam) for 1 h at room temperature with rotation. Bead-immunocomplexes were reversed cross-linked after RNA and protein digestion. DNA was then purified using 1.4X SPRI-select beads. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs) and sequenced on Aviti Cloudbreak Low 2x150 (250 M clusters/run). Input samples were generated alongside the immunoprecipitated (IP) samples. Exogenous chromatin (from Drosophila Schneider 2 (S2) cells), prepared with the same protocol was added to each reaction as spike-in.  Reads were processed, aligned, and normalized using QuasR, deepTools, and DESeq2 to generate coverage files and identify differential enrichment (https://github.com/Krebslabrep/TF-chromatin.git).
To test if H3K27Ac contributes to chromatin accessibility at enhancers, we globally reduced H3K27Ac levels by chemical inhibition of the histone acetylase p300 (with the small molecule A-485, final concentration 3 µM). This dataset includes ChIP-seq data for H3K27Ac with spike-in normalization, comparing DMSO and A-485 treated samples in mouse cells (i.e., XY 159 knock-out of the three DNA methyl transferases (DNMT TKO) mESCs). Two biological replicates were generated for each treatment condition. In summary, after treating the cells for 24h, cross-link ChIP-seq was performed. The protocol was adapted from (Trovato et al., 2024), with minor modifications. Chromatin was sheared using the Bioruptor Pico (Diagenode) and incubated with the antibody against H3K27ac (ab4729, Abcam) for 1 h at room temperature with rotation. Bead-immunocomplexes were reversed cross-linked after RNA and protein digestion. DNA was then purified using 1.4X SPRI-select beads. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs) and sequenced on Aviti Cloudbreak Low 2x150 (250 M clusters/run). Input samples were generated alongside the immunoprecipitated (IP) samples. Exogenous chromatin (from Drosophila Schneider 2 (S2) cells), prepared with the same protocol was added to each reaction as spike-in.  Reads were processed, aligned, and normalized using QuasR, deepTools, and DESeq2 to generate coverage files and identify differential enrichment (https://github.com/Krebslabrep/TF-chromatin.git).
European Bioinformatics Institute