{"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-16014"],"description":["We 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - 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 days","Library 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% FBS","Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were aligned to AJ851868/mm9 hybrid genome using bowtie 2.2.8 with --non-deterministic flag","Data Transformation - All GRO-seq libraries were downsampled normalized to the smallest read number among the GRO-seq libraries"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["GRO-seq"],"species":["Mus musculus"],"pubmed_authors":["Adam Yongxin Ye","Frederick Alt"],"additional_accession":[]},"is_claimable":false,"name":"GRO-seq for Linear RAG Scanning Mediates Editing of Igκ Variable Region Repertoires","description":"We 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.","dates":{"release":"2026-02-23T00:00:00Z","modification":"2026-05-27T12:28:51.214Z","creation":"2025-11-13T14:53:31.243Z"},"accession":"E-MTAB-16014","cross_references":{"ENA":["ERP183878"],"Biostudies":["E-MTAB-16001","E-MTAB-16007"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005227","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}