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Series GSE81274 Query DataSets for GSE81274
Status Public on Jun 26, 2016
Title Chromatin accessibility maps of chronic lymphocytic leukemia identify subtype-specific epigenome signatures and transcription regulatory networks
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
Summary Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, we established genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using the ATAC-seq assay, and we also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting dataset, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status – which distinguishes the two major subtypes of CLL – was accurately predicted by the chromatin profiles, and gene regulatory networks inferred for IGHV-mutated vs. IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we found widespread heterogeneity in the CLL chromatin landscape, established a community resource for studying epigenome deregulation in leukemia, and demonstrated the feasibility of chromatin accessibility mapping in cancer cohorts and clinical research.
 
Overall design Genome-wide profiling of chromatin states and gene expression levels in 88 CLL samples from 55 individuals gave rise to 88 ATAC-seq profiles, 40 ChIPmentation profiles (10 samples, each with 3 different antibodies and matched immunoglobulin control), and 10 RNA-seq profiles.

Raw sequence data has been deposited at the EBI's European Genome-phenome Archive (EGA) under the accession number EGAS00001001821 (controlled access to protect patient privacy).
Web link http://cll-chromatin.computational-epigenetics.org
 
Contributor(s) Rendeiro AF, Schmidl C, Strefford JC, Walewska R, Davis Z, Farlik M, Oscier D, Bock C
Citation(s) 27346425
Submission date May 10, 2016
Last update date Dec 23, 2018
Contact name Christoph Bock
E-mail cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (138)
GSM2148380 ATAC-seq for CLL patient 50, sample 1-5-35290
GSM2148382 ATAC-seq for CLL patient 244, sample 1-5-16241
GSM2148384 ATAC-seq for CLL patient 244, sample 1-5-33025
Relations
BioProject PRJNA321180

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
GSE81274_CLL_expression_matrix.csv.gz 591.2 Kb (ftp)(http) CSV
GSE81274_RAW.tar 28.7 Gb (http)(custom) TAR (of BIGWIG, NARROWPEAK)
Raw data not provided for this record
Processed data is available on Series record
Processed data provided as supplementary file

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