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Sample GSM740352 Query DataSets for GSM740352
Status Public on Sep 26, 2011
Title A11
Sample type genomic
 
Channel 1
Source name Mesothelioma tumor, biphasic
Organism Homo sapiens
Characteristics tissue: malignant pleural mesothelioma (MPM)
subtype: biphasic
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer's instructions.
Label Cy5
Label protocol Standard Agilent Cy5/Cy3 labeling protocols were used with 3ug of DNA.
 
Channel 2
Source name Promega normal reference
Organism Homo sapiens
Characteristics disease state: normal
sample type: reference
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer's instructions.
Label Cy3
Label protocol Standard Agilent Cy5/Cy3 labeling protocols were used with 3ug of DNA.
 
 
Hybridization protocol Labelled cDNA was hybridized to the arrays at 20rpm at 65C for 40 hours following Agilent instructions.
Scan protocol Slides were scanned using the Agilent Scanner with the standard protocols.
Description Genomic DNA from an MPM tumor for aCGH analysis.
Data processing The normalization is done through gcNormalization developed at MSKCC (http://cbio.mskcc.org/CGCC/methods_091022.pdf). The 'methods_091022.pdf' file is also linked to the Series record as a supplementary file.
 
Submission date Jun 10, 2011
Last update date Sep 26, 2011
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
 
Platform ID GPL9128
Series (2)
GSE29211 The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma
GSE29902 Mesothelioma tumor aCGH profiles

Data table header descriptions
ID_REF
VALUE Log2 (tumor/reference) value from gcNormalization

Data table
ID_REF VALUE
A_14_P100000 0.05148370845
A_14_P100001 0.07131424327
A_14_P100002 0.0493777956124398
A_14_P100003 0.0578885042
A_14_P100005 0.06615178446
A_14_P100006 0.0148693455790663
A_14_P100007 0.06085430576
A_14_P100008 0.06318092015
A_14_P100009 0.06755160415
A_14_P100010 0.03938586926
A_14_P100011
A_14_P100012 0.06682394233
A_14_P100013 -0.136894793446406
A_14_P100014 0.09401331232
A_14_P100015 0.04622889032
A_14_P100016 0.06827254165
A_14_P100017 0.08586307954
A_14_P100018 0.07249086451
A_14_P100019 -0.0361409818190171
A_14_P100020 0.07729110781

Total number of rows: 236385

Table truncated, full table size 6907 Kbytes.




Supplementary file Size Download File type/resource
GSM740352.txt.gz 61.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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