|
| Status |
Public on Sep 26, 2012 |
| Title |
GS000000658-ASM |
| Sample type |
genomic |
| |
|
| Source name |
Cell line_adenocarcinoma_smoker
|
| Organism |
Homo sapiens |
| Characteristics |
cell line name: H2122
other name: NCI-H2122
atcc #: CRL-5985
disease state: non-small cell lung cancer
tissue diagnosis: adenocarcinoma
gender: female
age: 46
race: Caucasian
smoking history: smoker
pack years: 30
cell line initiation date: 1989
source of speciment: pleural effusion
stage at initial evaluation: 4
death date: 1989
initial diagnosis date: 1989
|
| 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.
|
| |
|
| Hybridization protocol |
Hybridization was performed under contract by Illumina, Inc. per manufacturer's protocol.
|
| Scan protocol |
Scanning were performed under contract by Illumina, Inc. per manufacturer's protocol.
|
| Description |
130148
|
| 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.
|
| |
|
| 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] |
|
