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Sample GSM740345 Query DataSets for GSM740345
Status Public on Sep 26, 2011
Title A101
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 -0.155250708339986
A_14_P100001
A_14_P100002 0.104620744408918
A_14_P100003 -0.239219901830722
A_14_P100005 0.0693295210083675
A_14_P100006 0.0674595919404182
A_14_P100007 -0.0816130271460521
A_14_P100008 -0.147130416357516
A_14_P100009 0.0158866530053848
A_14_P100010 0.0460244940841359
A_14_P100011 0.0473825066746665
A_14_P100012 0.0176848045246862
A_14_P100013 -0.148211547015753
A_14_P100014 0.0744281813487285
A_14_P100015 -0.0129966156503631
A_14_P100016 0.0769961216500988
A_14_P100017 0.0901109947400985
A_14_P100018 0.0330039080861203
A_14_P100019 0.00149220894194857
A_14_P100020 0.100874022256416

Total number of rows: 236385

Table truncated, full table size 7700 Kbytes.




Supplementary file Size Download File type/resource
GSM740345.txt.gz 59.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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