|
| Status |
Public on Aug 31, 2016 |
| Title |
NSCLC_sample_196A |
| Sample type |
genomic |
| |
|
| Source name |
NSCLC tissue fresh frozen
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: non-small cell lung cancer
dead: 0
survival: 4505
age: 0
who performance status: 0
stadium: 1
smoking: 1
Sex: male
histology: Large cell carcinoma
cell line: crude cancer tissue
|
| Treatment protocol |
None
|
| Growth protocol |
human cancer tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were extracted from 2 to 10 frozen tissue sections (10 mm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany).
|
| Label |
Biotin
|
| Label protocol |
Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ).
|
| |
|
| Hybridization protocol |
Array experiments were performed according to the standard protocols for Affymetrix GeneChip® Mapping 250K Nsp I arrays (Gene Chip Mapping 500K Assay Manual, P/N 701930 Rev2., Affymetrix Inc., Santa Clara, CA, U.S.A. ). The arrays were then washed using Affymetrix fluidics stations.
|
| Scan protocol |
The arrays were scanned using the GeneChip® Scanner 3000 7G.
|
| Description |
Hybridized to 250K_Nsp
GSM707496
characteristics: dead survival status: alive=0, dead=1
characteristics: survival survival days
characteristics: age 0 (age < 70 ) versus 1 (age >= 70)
characteristics: WHO performance status 0 (status 0) versus 1 (status I-III)
characteristics: stadium 0 (stadium 1a and 1b) versus 1 (stadium 2a-IV)
characteristics: smoking 0 (non-smoker) versus 1 (smoker and ex-smoker)
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software.
Copy number values for individual SNPs were extracted and converted from CEL files using R package aroma.affymetrix v2.11.1.
The copy number values were calculated as 2*(sample chip effect/median reference chip effect). On X chromosome the information on the sex was used to assess plausible copy number estimates (men: sample chip effect/median male reference chip effect, women: 2*sample chip effect/median female reference chip effect). No segmentation perfermormed yet.
As reference data set 90 publicly available HapMap samples were used ((CEU), The International HapMap Consortium. The International HapMap Project. Nature 426, 789-796 (2003)).
|
| |
|
| Submission date |
Jan 11, 2016 |
| Last update date |
Jul 11, 2017 |
| Contact name |
Patrick Micke |
| E-mail(s) |
[email protected]
|
| Organization name |
Uppsala University
|
| Street address |
Rudbeck laboratory
|
| City |
Uppsala |
| ZIP/Postal code |
75185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE76730 |
Affymetrix SNP array data for NSCLC samples |
|
| Relations |
| Reanalysis of |
GSM707496 |
