|
Status |
Public on Sep 26, 2012 |
Title |
GS000000522-ASM |
Sample type |
genomic |
|
|
Source name |
Cell line_adenocarcinoma_smoker
|
Organism |
Homo sapiens |
Characteristics |
cell line name: H23 other name: NCI-H23 atcc #: CRL-5800 disease state: non-small cell lung cancer tissue diagnosis: adenocarcinoma gender: male age: 51 race: African American smoking history: smoker pack years: 40 cell line initiation date: 1976 source of speciment: lung death date: 1977 initial diagnosis date: 1976
|
Treatment protocol |
No treatments were performed prior to these assays.
|
Growth protocol |
Cells were grown in RPMI medium supplemented with 10% fetal calf serum. All cells were grown at 37°c and 5% CO2.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Extraction was performed under contract by Illumina, Inc. per manufacturer's protocol.
|
Label |
biotin
|
Label protocol |
Labeling was performed under contract by Illumina, Inc. per manufacturer's protocol.
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|
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Hybridization protocol |
Hybridization was performed under contract by Illumina, Inc. per manufacturer's protocol.
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Scan protocol |
Scanning were performed under contract by Illumina, Inc. per manufacturer's protocol.
|
Description |
129190
|
Data processing |
Genotype and normalized signal intensity were computed by Illumina's Genome Studio, V2011.1. A modified version of the PICNIC (PMID 19837654) algorithm computed total copy number and LOH as described previously (PMID 22895193). http://www.illumina.com/documents/products/technotes/technote_topbot.pdf Segmented_Absolute_Copy_Number; Segmented copy number for this SNP, where 2 is normal. PICNIC segmentation of data in the Absolute_Copy_Number column. Genotype; Genotype as called by GenomeStudio GC_SCORE; GenCall Score, genotyping quality from GenomeStudio Absolute_Copy_Number; Copy number for this SNP, where 2 is normal. Scaling from tumor/normal ratio to absolute copy number takes into account the overall sample ploidy, as estimated by the PICNIC algorithm. Segmented_Lesser_Parental_Copy_Number; PICNIC determines the copy number state for both parental alleles. For a normal autosome, one would expect one copy from each parent and the Segmented_Lesser_Parental_Copy_Number would then be 1. A value of zero represents LOH and values > 1 represent gain of both alleles. Raw data file column X; Signal intensity for X allele, as provided by GenomeStudio. Scaled to the same mean across array strips/sections. Raw data file column Y; Signal intensity for Y allele, as provided by GenomeStudio. Scaled to the same mean across array strips/sections.
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|
|
Submission date |
Sep 26, 2012 |
Last update date |
Sep 26, 2012 |
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 |
GPL16107 |
Series (1) |
GSE40908 |
Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events [array component] |
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