biostudies-arrayexpressAdam Yongxin YeMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16007We performed 3C-HTGTS 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.biostudies-arrayexpressSample Treatment - G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 daysNucleic Acid Extraction - Cells were fixed with 2% formaldehyde, quenched with glycine, lysed in a lysis buffer containing: 150mM NaCl, 0.5% NP-40, 1% Triton X-100, 50mM Tris-HCl pH7.5, 5mM EDTA pH8.0. Nuclei were digested with NlaIII, ligated with T4 DNA Ligase, treated with Proteinase K and RNase A prior to DNA precipitation.Sample Collection - Cells were fixed with 2% formaldehyde, quenched with glycine, lysed in a lysis buffer containing: 150mM NaCl, 0.5% NP-40, 1% Triton X-100, 50mM Tris-HCl pH7.5, 5mM EDTA pH8.0. Nuclei were digested with NlaIII, ligated with T4 DNA Ligase, treated with Proteinase K and RNase A prior to DNA precipitation.Library Construction - 3C-HTGTS libraries were prepared using linear-amplification PCR-mediated high-throughput genome-wide translocation sequencing protocol with indicated bait primersGrowth Protocol - v-Abl cell lines were cultured in RPMI1640 media with 15% FBSSequencing - 3C-HTGTS Final 3C-HTGTS libraries were sequenced on Illumina NextSeq550 or NextSeq2000 using a paired-end 150-bp sequencing kitOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - 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 (AJ851868/mm9 hybrid 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 bpData Transformation - All 3C-HTGTS libraries were normalized to 65488 total junctions, which represents the smallest recovered number of junctions among the 3C-HTGTS libraries that were compared.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 550DNA-seqMus musculusAdam Yongxin YeFrederick Altfalse3C-HTGTS for Linear RAG Scanning Mediates Editing of Igκ Variable Region RepertoiresWe performed 3C-HTGTS 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.2026-02-23T00:00:00Z2026-05-27T14:14:36.681Z2025-11-06T12:28:30.884ZE-MTAB-16007ERP189011E-MTAB-16001EFO_0002944EFO_0004170EFO_0003789EFO_0002693EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969