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Series GSE47766 Query DataSets for GSE47766
Status Public on Aug 05, 2013
Title Deep sequencing of the murine Igh repertoire reveals complex regulation of non-random V gene rearrangement frequencies
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary A diverse antibody repertoire is formed through the rearrangement of V, D, and J segments at the immunoglobulin heavy chain (Igh) loci. The C57BL/6 murine Igh locus has over 100 functional VH gene segments that can recombine to a rearranged DJH. While the non-random usage of VH genes is well documented, it is not clear what elements determine recombination frequency. To answer this question we conducted deep sequencing of 5’-RACE products of the Igh repertoire in pro-B cells, amplified in an unbiased manner. ChIP-seq results for several histone modifications and RNA polymerase II binding, RNA-seq for sense and antisense non-coding germline transcripts, and proximity to CTCF and Rad21 sites were compared to the usage of individual V genes. Computational analyses assessed the relative importance of these various accessibility elements. These elements divide the Igh locus into four epigenetically and transcriptionally distinct domains, and our computational analyses reveal different regulatory mechanisms for each region. Proximal V genes are relatively devoid of active histone marks and non-coding RNA in general, but having a CTCF site near their RSS is critical, suggesting that position near the base of the chromatin loops is important for rearrangement. In contrast, distal V genes have high levels of histone marks and non-coding RNA, which may compensate for their poorer RSS and for being distant from CTCF sites. Thus, the Igh locus has evolved a complex system for the regulation of V(D)J rearrangement that is different for of each the four domains that comprise this locus.
 
Overall design For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina HiSeq2000.
 
Contributor(s) Choi NM, Loguercio S, Su AI, Feeney AJ
Citation(s) 23898036
Submission date Jun 10, 2013
Last update date May 15, 2019
Contact name Salvatore Loguercio
Organization name TSRI
Department MB
Lab Balch
Street address 10550 North Torrey Pines Rd
City La Jolla
State/province California
ZIP/Postal code 92121
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (12)
GSM1156657 H3ac ChIP-seq
GSM1156658 H3K27me3 ChIP-seq
GSM1156659 H3ac H3K27me3 input control
Relations
BioProject PRJNA207764
SRA SRP024385

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Supplementary file Size Download File type/resource
GSE47766_RAW.tar 3.5 Gb (http)(custom) TAR (of BED, BW, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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