{"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-16001"],"description":["We performed HTGTS-V(D)J-seq in BM B cells and v-Abl transformed pro-B cells and its various mutant derivatives to study the molecular mechanisms of Igk secondary V(D)J recombination."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.2% SDS, 10mM Tris-HCl pH7.4, 2mM EDTA pH8.0, 200ug/ml proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.4, 0.5mM EDTA pH8.0","Sequencing - HTGTS-V(D)J-seq The final libraries were sequenced on Illumina NextSeq550 or NextSeq2000 using a paired-end 150-bp sequencing kit.","Growth Protocol - v-Abl cell lines were cultured in RPMI1640 media with 15% FBS","Sample Treatment - RAG complementation was performed by infecting v-Abl cell lines with RAG2 retrovirus followed by selection with puromycin G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 days","Sample Collection - Pre-B cells were isolated from 129SV WT or Cer/Sis-deleted mouse bone marrow by FACS sorting for B220+ CD43low IgM- cells Immature B cells were isolated from iPSC chimera-derived bone marrow by FACS sorting for B220+ CD19+ IgM- IgG1+ cells","Library Construction - HTGTS-V(D)J-seq libraries were prepared using linear-amplification PCR-mediated high-throughput genome-wide translocation sequencing protocol with indicated bait primers"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Standard basecalling formats for Miseq reads Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment We used a best-path searching algorithm to select the optimal sequence of alignments that describe the reads composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp","Sequence Alignment - mm9 genome, AJ851868/mm9 hybrid genome and indicated custom genomes"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["DNA-seq"],"species":["Mus musculus"],"pubmed_authors":["Adam Yongxin Ye","Frederick Alt"],"additional_accession":[]},"is_claimable":false,"name":"HTGTS for Linear RAG Scanning Mediates Editing of Igκ Variable Region Repertoires","description":"We performed HTGTS-V(D)J-seq in BM B cells and v-Abl transformed pro-B cells and its various mutant derivatives to study the molecular mechanisms of Igk secondary V(D)J recombination.","dates":{"release":"2026-02-23T00:00:00Z","modification":"2026-05-27T03:11:56.406Z","creation":"2025-11-04T09:06:19.44Z"},"accession":"E-MTAB-16001","cross_references":{"ENA":["ERP183653"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002693","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}