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Sample GSM517034 Query DataSets for GSM517034
Status Public on May 27, 2010
Title HF-23896-(1), Agilent
Sample type genomic
 
Channel 1
Source name HF-23896-(1)
Organism Homo sapiens
Characteristics organ: Lung Cancer
Extracted molecule genomic DNA
Extraction protocol Qiagen AllPrep extraction kit was used according to the manufacturer's instructions
Label Cy5
Label protocol Agilent's Genomic DNA Labeling Kit Plus
 
Channel 2
Source name male genomic DNA (Promega P/N G1471)
Organism Homo sapiens
Characteristics reference: male genomic DNA (Promega P/N G1471)
Extracted molecule genomic DNA
Extraction protocol Qiagen AllPrep extraction kit was used according to the manufacturer's instructions
Label Cy3
Label protocol Agilent's Genomic DNA Labeling Kit Plus
 
 
Hybridization protocol Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol
Scan protocol Agilent's user manual (Agilent scanner)
Description Tumor vs. Normal
Data processing Tumor samples were assayed on Agilent Human Genome CGH 244A Microarrays. Human male genomic DNA (Promega P/N G1471) was used as reference. Individual log2 ratios of background subtracted signal intensities were obtained from the Agilent Feature Extraction software version 9.5. The log2 ratios were centered to a median of zero and the resulting log2 ratio values for each probe were segmented using GLAD [3]. All probes within the genomic bounds of a given GLAD-derived segment were given the mean copy number value of probes within that segment.
 
Submission date Mar 01, 2010
Last update date May 24, 2010
Contact name Peter Haverty
E-mail(s) phaverty@gene.com
Organization name Genentech, Inc.
Department Bioinformatics
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platform ID GPL9128
Series (2)
GSE20574 Agilent 244A aCGH array for comparison of lung tumor CNA to high-throughput sequencing data
GSE20585 The mutation spectrum revealed by paired genome sequences from a lung cancer patient

Data table header descriptions
ID_REF
VALUE GLAD segmented copy number

Data table
ID_REF VALUE
A_14_P112718 1.84363889694214
A_16_P15000916 1.84363889694214
A_16_P15001074 1.84363889694214
A_16_P00000012 1.84363889694214
A_16_P00000014 1.84363889694214
A_16_P00000017 1.84363889694214
A_16_P00000021 1.84363889694214
A_16_P00000023 1.84363889694214
A_16_P00000027 1.84363889694214
A_16_P00000033 1.84363889694214
A_16_P35001586 1.84363889694214
A_16_P15001533 1.84363889694214
A_16_P00000060 1.84363889694214
A_16_P15001594 1.84363889694214
A_16_P00000082 1.84363889694214
A_16_P00000090 1.84363889694214
A_16_P00000099 1.84363889694214
A_16_P15001666 1.84363889694214
A_16_P00000112 1.84363889694214
A_16_P00000114 1.84363889694214

Total number of rows: 235834

Table truncated, full table size 7274 Kbytes.




Supplementary file Size Download File type/resource
GSM517034.txt.gz 73.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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