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Series GSE138135 Query DataSets for GSE138135
Status Public on Aug 24, 2020
Title Igk locus capture-based target enrichment sequencing
Organism Mus musculus
Experiment type Other
Summary Cell cycle is a major determinant of DNA double-strand break (DSB) repair pathway choice with homologous recombination (HR) that is most active in S phase cells and non-homologous end-joining (NHEJ) that dominates in G1 phase cells. A third less well-defined mechanism, 'alternative end-joining', has been shown to promote error-prone repair in NHEJ- or HR-deficient cells. Here, we have used a physiologic system of NHEJ-mediated genomic rearrangements induced by the site-specific RAG1/2 endonuclease in G1 cells to investigate the fate of unrepaired G1 DSBs upon entry into the cell cycle. We show that, in the absence of XRCC4, alternative end-joining rescues RAG-induced DSB repair and promotes chromosome translocations upon G1 cell cycle exit.
 
Overall design Coding and signal sequences of 140 mouse Igk V and 5 Igk J segments were downloaded from MGI database. 280 bps windows flanking recombination signal site (RSSs) of Igk V and J segments, including coding and signal sequences, were used to design Agilent SureSelect customized probes (Agilent Technologies). A total of 2348 120-mer probes (1168 for signal ends; 1180 for coding ends) were designed for Igk locus capture. SureSelectXT Target Enrichment System kit (Agilent Technologies) was used to prepare Igk locus capture sequencing libraries.
 
Contributor(s) Yu W, Lescale C, Deriano L
Citation(s) 33067475
Submission date Sep 30, 2019
Last update date Oct 27, 2020
Contact name Ludovic Deriano
E-mail(s) ludovic.deriano@pasteur.fr
Organization name Institut Pasteur
Department Immunology
Lab Lymphocyte Development and Oncogenesis
Street address 25-28 Rue du Docteur Roux
City Paris
ZIP/Postal code 75015
Country France
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (3)
GSM4100877 Xrcc4-/- p53-/- non-treatment
GSM4100878 Xrcc4-/- p53-/- ABLKi
GSM4100879 Xrcc4-/- p53-/- Released
This SubSeries is part of SuperSeries:
GSE138137 High-throughput sequencing of RAG induced re-arrangements
Relations
BioProject PRJNA574914
SRA SRP223673

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE138135_RAW.tar 190.0 Kb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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