{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Christophe RACHEZ"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15197"],"description":["Chromatin accessibility assay by ATACseq in BMEL cells. Three clones (TKO1, TKO2, TKO3) of BMEL TKO cells invalidated for the expression of the three HP1 isoforms (Cbx1-/-; Cbx3-/-; Cbx5-/-) were compared to three clones (Het1, Het32, Het35) of BMEL Het cells (Cbx1+/+; Cbx3+/+; Cbx5+/-) as controls."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Chromatin accessibility assays, including library construction, on Het1, Het32, Het35, TKO1, TKO2, TKO3 were performed with an ATACseq kit (ActiveMotif, 53150) according to the manufacturer's instructions.","Sequencing - Paired-end sequencing (9G raw data/sample) of the dual-index ATACseq libraries was performed by Novogene (UK) Co., Ltd.","Sample Collection - Chromatin accessibility assays on Het1, Het32, Het35, TKO1, TKO2, TKO3 were performed with an ATACseq kit (ActiveMotif, 53150) according to the manufacturer's instructions.","Nucleic Acid Extraction - Chromatin accessibility assays, including nucleic acid extraction, on Het1, Het32, Het35, TKO1, TKO2, TKO3 were performed with an ATACseq kit (ActiveMotif, 53150) according to the manufacturer's instructions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Bigwig files were generated from BAM files with bamCoverage (parameter: –normalizeUsing CPM) from Deeptools (v3.1.3)","Sequence Alignment - ATACseq reads were mapped to mm10 using bowtie2 with the parameters --very-sensitive -X 2000 --maxins 500 --no-discordant --no-mixed -k 1. Aligned BAM files were sorted and indexed using SAMtools (v1.8)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["ATAC-seq"],"species":["Mus musculus"],"pubmed_authors":["Christophe RACHEZ"],"additional_accession":[]},"is_claimable":false,"name":"ATACseq in BMEL cells invalidated or not for the expression of the three HP1 isoforms (CBX1, CBX3, CBX5)","description":"Chromatin accessibility assay by ATACseq in BMEL cells. Three clones (TKO1, TKO2, TKO3) of BMEL TKO cells invalidated for the expression of the three HP1 isoforms (Cbx1-/-; Cbx3-/-; Cbx5-/-) were compared to three clones (Het1, Het32, Het35) of BMEL Het cells (Cbx1+/+; Cbx3+/+; Cbx5+/-) as controls.","dates":{"release":"2026-03-31T00:00:00Z","modification":"2026-03-31T01:03:46.847Z","creation":"2025-06-04T19:05:07.363Z"},"accession":"E-MTAB-15197","cross_references":{"ENA":["ERP173170"],"Biostudies":["E-MTAB-15196","E-MTAB-15194"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}