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Series GSE29902 Query DataSets for GSE29902
Status Public on Sep 26, 2011
Title Mesothelioma tumor aCGH profiles
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Malignant pleural mesotheliomas (MPMs) often show CDKN2A and NF2 inactivation but other highly recurrent mutations have not been described. To identify additional driver genes, we used an integrated genomic analysis of 53 MPM tumor samples to guide a focused sequencing effort that uncovered somatic inactivating mutations in BAP1 in 23% of MPM. The BAP1 nuclear deubiquitinase is known to target histones (together with ASXL1 as a Polycomb repressor subunit) and the HCF1 transcriptional co-factor, and we show that BAP1 knockdown in MPM cell lines affects E2F and Polycomb target genes. These findings implicate transcriptional deregulation in the pathogenesis of MPM.
 
Overall design DNA from 53 malignant pleural mesothelioma tumors was collected and hybridized to aCGH arrays. Data were analyzed to create gain and loss profiles for each tumor.

This submission includes gcNormalized-data.
 
Contributor(s) Ladanyi M, Bott M
Citation(s) 21642991
Submission date Jun 10, 2011
Last update date Nov 14, 2014
Contact name Yupu Liang
E-mail(s) liangy@rockefeller.edu
Organization name The Rockefeller University
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL9128 Agilent-014693 Human Genome CGH Microarray 244A (Probe name version)
Samples (53)
GSM740344 A100
GSM740345 A101
GSM740346 A102
This SubSeries is part of SuperSeries:
GSE29211 The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma
Relations
BioProject PRJNA142825

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
GSE29902_RAW.tar 3.1 Gb (http)(custom) TAR (of TXT)
GSE29902_methods_091022.pdf.gz 195.8 Kb (ftp)(http) PDF
Processed data included within Sample table

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