GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE138136 Query DataSets for GSE138136
Status Public on Aug 24, 2020
Title High-throughput capture of cis-rearrangement and trans-rearrangement sequence [LAM-HTGTS]
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 We performed linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) on mouse v-Abl/Bcl2  immortalized pro-B cell lines which included genotypes WT, Xrcc4-/-, p53-/- and Xrcc4-/- p53-/-. Igk-J4 primer was used as bait to capture cis-rearrangement sequence within Igk loci and trans-rearrangement sequence with whole genome-wide. The captured of cis- and trans-rearrangement sequences with Igk-J4 were analyzed and compared among cycling cells, v-Abl kinase inhibitor treated and released cells.

*Please note that each wig processed data was generated from all replicates together and is linked to the corresponding rep1 sample records.
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
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 (32)
GSM4100880 WT non-treatment rep1
GSM4100881 WT non-treatment rep2
GSM4100882 Xrcc4-/- p53-/- non-treatment rep1
This SubSeries is part of SuperSeries:
GSE138137 High-throughput sequencing of RAG induced re-arrangements
BioProject PRJNA574913
SRA SRP223675

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
GSE138136_RAW.tar 2.0 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap