biostudies-arrayexpressAdam Yongxin YeMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16014We performed Gro-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.biostudies-arrayexpressSequencing - GRO-seq libraries were prepared from the G1-arrested, RAG2-deficient v-Abl cell lines as described, sequenced using Illumina NextSeq2000 using paired-end 150-bp sequencing kits, and processed with a previously described pipeline.Sample Treatment - G1-arrest was performed by treating v-Abl cell lines with 3uM STI for 4 daysLibrary Construction - Illumina adapters were ligated to RNA followed by cDNA generation with reverse transcriptase. Libraries were PCR-amplified with Illumina primers and subjected to sequencing.Growth Protocol - v-Abl cell lines were cultured in RPMI1640 media with 15% FBSSample Collection - Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction.Nucleic Acid Extraction - Briefly, 10 million cells were permeabilized with permeabilization buffer (10 mM Tris-HCl, pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, one tablet of protease inhibitors per 50 ml and 4 units Rnase inhibitor per ml) and resuspended in 100 ul storage buffer (10 mM Tris-HCl, pHHH 8.0, 25% (vol/vol) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT). Permeabilized cells were subjected to nuclear run-on (2xRun-on mix: 5 mM Tris-Cl, PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, 10 units of RNase inhibitor, 1% sarkosyl) at 37o for 5 min, followed by Trizol-based RNA extraction.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads were aligned to AJ851868/mm9 hybrid genome using bowtie 2.2.8 with --non-deterministic flagData Transformation - All GRO-seq libraries were downsampled normalized to the smallest read number among the GRO-seq librariesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000GRO-seqMus musculusAdam Yongxin YeFrederick AltfalseGRO-seq for Linear RAG Scanning Mediates Editing of Igκ Variable Region RepertoiresWe performed Gro-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.2026-02-23T00:00:00Z2026-05-27T12:28:51.214Z2025-11-13T14:53:31.243ZE-MTAB-16014ERP183878E-MTAB-16001E-MTAB-16007EFO_0002944EFO_0004170EFO_0003789EFO_0005227EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969