Project description:Bait-capture based Single Molecule Footprinting (SMF) data. SMF data is obtained by treating extracted nuclei with a GpC and a CpG methyltransferase, where binding of proteins on DNA, e.g. nucleosomes and transcription factors (TFs), leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from two F1 hybrid embryonic stem cells (ES) obtained by crossing C57BL/6NJ with CAST/EiJ and SPRET/EiJ, respectively. The resulting cell line were underwent triple genetic knockout for the endogenous methyltransferase enzymes (DNMT TKO). Sequencing libraries were prepared using Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for cis-regulatory regions of the mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types.
Project description:Bait-capture based Single Molecule Footprinting (SMF) data from Kreibich et al., 2022. SMF data is obtained by treating extracted nuclei with a GpC methyltransferase, where binding of proteins on DNA, e.g. nucleosomes and transcription factors (TFs), leave behind unmethylated GpCs as footprints. Data in this experiment comprises SMF data obtained from WT embryonic stem cells (ES), DNMT TKO ES, TET TKO ES, F1 hybrid ES (129/CAST), neural progenitor (NP),�myoblast (C2C12) and�murine erythroleukemia (MEL)�cells. These data were generated by employing Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for cis-regulatory regions of the mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types. The SMF procedure maintains the endogenous DNA methtylation in CpG context, allowing the simultaneous detection of chromatin accessibility, TF binding and endogenous DNA methylation.
Project description:Bait-capture based Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES, DNMT-TKO, and neural progenitor (NP) cells. These data were generated by employing Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for regulatory regions of mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types.
Project description:Bait-capture based Single Molecule Footprinting (SMF) data. SMF data is obtained by treating extracted nuclei with a GpC and a CpG methyltransferase, where binding of proteins on DNA, e.g. nucleosomes and transcription factors (TFs), leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from a previously reported Sox2 degron mESC line (see PMID: 33318687). Sequencing libraries were prepared using Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for cis-regulatory regions of the mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types.
Project description: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.