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Sample GSM740348 Query DataSets for GSM740348
Status Public on Sep 26, 2011
Title A105
Sample type genomic
 
Channel 1
Source name Mesothelioma tumor, Sarc
Organism Homo sapiens
Characteristics tissue: malignant pleural mesothelioma (MPM)
subtype: Sarc
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 -0.187871070419642
A_14_P100001 0.139224354602841
A_14_P100002 0.104912505782959
A_14_P100003 -0.0844045685551864
A_14_P100005 0.0247438396469188
A_14_P100006 -0.0701095292968436
A_14_P100007 -0.104000049073181
A_14_P100008 -0.00791655299271263
A_14_P100009 0.213523282111492
A_14_P100010 0.0521270202067816
A_14_P100011 0.158055591914426
A_14_P100012 0.110013017169528
A_14_P100013 -0.0201586882770775
A_14_P100014 -0.040264620156614
A_14_P100015 0.08003299875802
A_14_P100016 -0.0567110576607031
A_14_P100017 -0.0141658421390797
A_14_P100018 0.101251065727543
A_14_P100019 0.0204205117874318
A_14_P100020 -0.122874172284936

Total number of rows: 236385

Table truncated, full table size 7561 Kbytes.




Supplementary file Size Download File type/resource
GSM740348.txt.gz 59.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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