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Bait-capture based single molecule footprinting in 159 DNMT TKO mESCs upon p300 inhibition

ABSTRACT: 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 bait capture single molecule footprinting (SMF) data, 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). Three biological replicates were generated for each treatment condition. In summary, after 24 hours of treatment, cells were collected for SMF, which marks accessible cytosines via recombinant methyltransferases, followed by bisulfite sequencing to infer protein-DNA interactions and chromatin accessibility at single-molecule resolution. Libraries were prepared using the Agilent SureSelect Mouse Methyl-Seq kit, which enriches for cis-regulatory elements, and sequenced on an Illumina NextSeq platform (150 bp paired-end, high-output mode). Reads were pre-processed with TrimGalore, aligned using QuasR, and deduplicated with Picard’s MarkDuplicates tool. Further analyses were conducted using custom scripts available at https://github.com/Krebslabrep/TF-chromatin.git.

INSTRUMENT(S): Illumina MiSeq, NextSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: charles girardot

PROVIDER: E-MTAB-17191 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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