Dataset features

Specifications


Dataset type: Other
Number of samples: 16
Release date: Jul 26 2018
Last update date: Oct 17 2018
Access: Public
Diseases: Congenital Abnormalities
Dataset link Kinase-dependent structural role of DNA-PKcs during immunoglobulin class switch recombination

Experimental Protocol


To ascertain how different DNA-PKcs mutations (null vs KD) affect CSR in an isotype dependent manner, we employed the High Throughput Genome Translocation Sequencing (HTGTS) (1) method to analyze CSR junctions in DNA-PKcsKD/KD and DNA-PKcs-/- B cells with preassembly IgH and L chains (HL). We measured switching efficiency, efficiency and size of small MH in DNA-PKcs-/- and DNA-PKcsKD/KD B cells in contrast to cNHEJ-deficient Xrcc4-/- B cells, as well as insertions and deletions than both Sμ-Sμ and Sμ-Sε junctions. Finally our analyses also identified long MH mediated inter-chromosomal translocations in DNA-PKcsKD/KD B cells and a reduced number of G mutations in 5’Sμ in repair deficient B cells. Since all our experimental mice carry the preassembled IgH on the 129 ackground, we replaced the IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6-based mm9 with the corresponding region in the AJ851868.3 (NCBI gene accession no. AJ851868.3) 129 IgH sequence (1415966–1592715) to generate the mm9sr (switch region replacement) genome. 1. Hu J, et al. (2016) Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc 11:853–871.

Repositories


GEO

GSE117628

ENA

SRP155142

BioProject

PRJNA482753

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Contact


Zhengping Shao