biostudies-arrayexpressMisbah AbbasMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13559ATAC-seq experiments were performed to map the open chromatin regions of embryonic stem cells and neural stem cells.biostudies-arrayexpressGrowth Protocol - ES (2i/LIF) cells were grown on gelatin-coated culture plastic in embryonic stem cells medium in the presence of MEK inhibitor (PD0325901) and GSK3 inhibition (CHIR99021) with LIF to maintain ESCs in a naive ground state. Cells were split at 80% confluence with a density of 30000 cells/sq.cm. The medium was exchanged daily.Sample Collection - Cells were detached with Accutase, counted and 100,000 cells were immediately used for the ATAC-seq experiments.Growth Protocol - NS cells were grown on laminin-coated plates in neural differentiation medium containing N2 and B27 supplements along with recombinant murine EGF and bFGF to a final concentration of 10 ng/ml. Cells were split at 80% confluence with a density of 35000 cells/sq.cm. The medium was exchanged daily.Library Construction - ATAC-seq procedure was performed with ATAC-Seq kit (Active Motif, 53150), according to manufacturer's instructions.Sequencing - Sequencing was performed Illumina 6000 platform in paired-end, 100 bp mode.Sample Treatment - CTCF depletion was carried out in CTCF-AID-GFP ES and NS Cells by treating with 500uM of indole acetic acid (IAA) dissolved in culture media for 24hOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - We aligned reads to this mouse reference genome (mm10) using bowtie2 with default options.Data Transformation - We used the bamCoverage tool from the deeptools suite to generate bigwig tracks using the default parameters, and normalised using 'RPGC'MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000ATAC-seqMus musculusBondita DehingiaMałgorzata MilewskaAleksandra PękowskaDebadeep ChaudhuryMisbah AbbasfalseATAC-seq from mouse embryonic stem cell and their derivative neural stem cellsATAC-seq experiments were performed to map the open chromatin regions of embryonic stem cells and neural stem cells.2025-06-13T00:00:00Z2025-06-13T14:02:34.27Z2023-11-22T23:06:47.103ZE-MTAB-13559ERP155376E-MTAB-13558E-MTAB-13560E-MTAB-13561E-MTAB-13562EFO_0007045EFO_0004170EFO_0003789EFO_0004917EFO_0003816EFO_0005518EFO_0004184EFO_0003969