{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Mingxia Li"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ATAC-seq"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-10593"],"description":["Genome-wide measurements of chromatin accessibility in MC38 colon carcinoma cells and MC38 Bap1-knockout cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on Illumina NovaSeq 6000 machines with 150 bp pair end mode. Adapters in the reads were trimmed using fastp (PMID 30423086) with the “--detect_adapter_for_pe” flag.","Library Construction - Adapters in the reads were trimmed using fastp (PMID 30423086) with the “--detect_adapter_for_pe” flag. The trimmed reads were aligned to the mouse reference genome (mm10) using hisat2 (PMID 3137580) with the “--no-temp-splicesite --no-spliced-alignment” flags.","Nucleic Acid Extraction - The DNA in the nucles was processed by transposition reaction using Tn5 Transposase and purified follow the instructions.","Sample Collection - After the 1000u/ml IFN-β stimulation for 48 hours, the tumor were collected and lysed in order to extract the cell nucleus."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Mingxia Li"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-Seq analysis of MC38 colon carcinoma cells and MC38 Bap1-knockout cells","description":"Genome-wide measurements of chromatin accessibility in MC38 colon carcinoma cells and MC38 Bap1-knockout cells.","dates":{"release":"2025-07-06T00:00:00Z","modification":"2023-07-10T16:30:55.446Z","creation":"2023-07-10T16:30:55.446Z"},"accession":"E-MTAB-10593","cross_references":{"ENA":["ERP149375"],"Biostudies":["E-MTAB-10588","E-MTAB-10610","E-MTAB-10587","E-MTAB-10585","E-MTAB-10584"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0005518","EFO_0004184"]}}