{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Misbah Abbas"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13560"],"description":["H3K27ac ChIP-Seq experiment was performed to map and compare potential changes in elements of mouse embryonic stem cells and their derived neural stem cells"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth 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.","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 - Libraries were constructed using Ovation Ultra System V2 (Tecan, 0344NB-32), according to manufacturer's instructions.","Sequencing - Sequencing was performed using Illumina 6000 platform in paired-end, 100bp mode.","Sample Collection - Cells were detached with Accutase, counted and crosslinked with 1% (final) formaldehyde in their medium. Reaction was quenched with 0.125M (final) glycine, cell pellets were washed with PBS, snap frozen and stored in -80 freezer. Pellet of 3 million cells was used for H3K27A ChIP experiment.","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 24h","Nucleic Acid Extraction - ChIP prodecure was performed as described before (Pekowska et al., 2018, Cell)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence 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'"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"species":["Mus musculus"],"pubmed_authors":["Bondita Dehingia","Małgorzata Milewska","Aleksandra Pękowska","Debadeep Chaudhury","Misbah Abbas"],"additional_accession":[]},"is_claimable":false,"name":"H3K27ac ChIP-seq from mouse embryonic stem cell and their derivative neural stem cells","description":"H3K27ac ChIP-Seq experiment was performed to map and compare potential changes in elements of mouse embryonic stem cells and their derived neural stem cells","dates":{"release":"2025-06-13T00:00:00Z","modification":"2025-06-13T14:03:13.588Z","creation":"2023-11-22T23:08:15.772Z"},"accession":"E-MTAB-13560","cross_references":{"ENA":["ERP155377"],"Biostudies":["E-MTAB-13558","E-MTAB-13559","E-MTAB-13561","E-MTAB-13562"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0004917","EFO_0003816","EFO_0005518","EFO_0004184","EFO_0003969"]}}