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Series GSE79892 Query DataSets for GSE79892
Status Public on Aug 04, 2016
Title Orientation-specific RAG activity in chromosomal loop domain contribute to Tcrd V(D)J recombination during T cell development
Organism Mus musculus
Experiment type Other
Summary T cell antigen receptor δ (Tcrd) variable region exons are assembled by RAG-initiated V(D)J recombination. Here, we employ a high throughput method to map hundreds of thousands of RAG-initiated Tcrd D segment (Trdd1 and Trdd2) rearrangements in developing thymocytes. We find that Trdd2 joins directly to Trdv, Trdd1, and Trdj segments, but Trdd1 joining is ordered with joining to Trdd2 a prerequisite for further rearrangement. We also find frequent, previously unappreciated Trdd1 and Trdd2 rearrangements that inactivate Tcrd. Moreover, we find numerous RAG off-targets that are generated via unidirectional RAG tracking across the loop-domain containing Trdd1, Trdd2 and Trdj. Correspondingly, disruption of the upstream domain boundary causes spreading of on- and off-target RAG activity to the proximal Trdv domain.
 
Overall design RAG-initiatd Tcrd D segment rearrangements in developing thymocytes were generated by deep sequencing using illumine Miseq
 
Contributor(s) Zhao L, Alt FW
Citation(s) 27526713
Submission date Apr 04, 2016
Last update date May 15, 2019
Contact name Lijuan Zhao
E-mail(s) lexieljzhao@gmail.com
Phone 617-606-0189
Organization name Boston Children's Hospital
Lab Frederick W. Alt
Street address 1 Blackfan Circle
City Boston
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (31)
GSM2107911 Trdd2_5P_WT_rep1
GSM2107912 Trdd2_5P_WT_rep2
GSM2107913 Trdd2_5P_WT_rep3
Relations
BioProject PRJNA317332
SRA SRP072839

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Supplementary file Size Download File type/resource
GSE79892_RAW.tar 72.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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