{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Adam Yongxin Ye"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16602"],"description":["We performed ATAC-seq in v-Abl transformed pro-B cells and its various mutant derivatives to study the differential molecular mechanisms of Igk secondary V(D)J recombination."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 days","Library Construction - Libraries were PCR-amplified with Illumina primers and subjected to sequencing.","Growth Protocol - v-Abl cell lines were cultured in RPMI1640 media with 15% FBS","Sample Collection - 50,000 G1-arrested RAG-deficient v-Abl cells were used for experiment","Nucleic Acid Extraction - Briefly, the collected G1-arrest live cells were used for cell lysis, nuclei preparation, tagmentation by Tn5 and library amplification according to Zymo-Seq ATAC Library Kit (D5458).","Sequencing - ATAC-Seq Final ATAC-Seq libraries were sequenced on Illumina NextSeq2000"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were processed using Nextflow ATAC-seq pipeline (https://github.com/nf-core/atacseq)","Data Transformation - All bigWig files were scaling normalized to 1 million mapped reads."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["ATAC-seq"],"species":["Mus musculus"],"pubmed_authors":["Adam Yongxin Ye","Frederick Alt"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-seq for Linear RAG Scanning Mediates Editing of Igκ Variable Region Repertoires","description":"We performed ATAC-seq in v-Abl transformed pro-B cells and its various mutant derivatives to study the differential molecular mechanisms of Igk secondary V(D)J recombination.","dates":{"release":"2026-02-23T00:00:00Z","modification":"2026-05-27T13:42:23.508Z","creation":"2026-01-29T13:07:18.971Z"},"accession":"E-MTAB-16602","cross_references":{"ENA":["ERP188307"],"Biostudies":["E-MTAB-16001","E-MTAB-116007","E-MTAB-16014"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}