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Series GSE34316 Query DataSets for GSE34316
Status Public on Jul 16, 2012
Title Genome-wide Detection of Genes Targeted by Aberrant Somatic Hypermutation in Lymphoma
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We report a novel approach to identify genome-wide somatic hypermutation hotspots from short Illumina H3K4me3 ChIPseq reads in diffuse large B-cell lymphoma cells (DLBCL). Abberant somatic hypermation are known to occur at the promoters of several proto-oncogenes in DLBCL. To identify such events genome-wide, we performed H3K4me3 ChIPseq experiments (as to enrich promoter sequences of actively transcribed genes) in 2 DLBCL cells lines (OCI-Ly1 and OCI-Ly8) and their normal B-cell counterparts, Naive B cells (NBC) and Germinal Center B cells (GCBs). We discover new genes that harbor mutations in their promoter regions that are potentially introduced by the aberrant activation-induced cytosine deaminase activity in lymphoma cell lines, and many of these genes are important for the B cell biology. Moreover, we show that these mutations can affect the activities of these promoters. Our study provides a feasible approach for the detection of promoter mutations and broadens our knowledge on promoter mutations in lymphomas.
Overall design Examination of 1 histone mark (H3K4me3) in 4 different cell types.
Contributor(s) Jiang Y
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Submission date Dec 09, 2011
Last update date May 15, 2019
Contact name Yanwen Jiang
Organization name Weill Cornell Medical College
Street address 413 E. 69th St. BB1462
City New York
State/province NY
ZIP/Postal code 10021
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM847242 OCI-Ly1-H3K4me3-ChIPseq
GSM847243 OCI-Ly8-H3K4me3-ChIPseq
GSM847244 NBC-H3K4me3-ChIPseq
SRA SRP009676
BioProject PRJNA151499

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
GSE34316_RAW.tar 9.4 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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