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Sample GSM740359 Query DataSets for GSM740359
Status Public on Sep 26, 2011
Title A28
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 0.5846556682
A_14_P100001 0.486602081
A_14_P100002 0.0720817834863386
A_14_P100003 0.5496905815
A_14_P100005 0.3191661196
A_14_P100006 0.0266887328647573
A_14_P100007 0.7373991286
A_14_P100008 0.8511798229
A_14_P100009 0.4305849488
A_14_P100010 0.203179061
A_14_P100011
A_14_P100012 0.6366000481
A_14_P100013 -0.0756541305901013
A_14_P100014 0.9616164108
A_14_P100015 0.4433183913
A_14_P100016 0.5876028204
A_14_P100017 0.5081014358
A_14_P100018 0.4241125532
A_14_P100019 0.0350711484570381
A_14_P100020 0.6704381977

Total number of rows: 236385

Table truncated, full table size 6739 Kbytes.




Supplementary file Size Download File type/resource
GSM740359.txt.gz 60.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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