|
| Status |
Public on Nov 01, 2011 |
| Title |
Squamous_cell_carcinoma_sample_300A |
| Sample type |
genomic |
| |
|
| Source name |
Non-small cell lung cancer tissue, long-term survival, squamous cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: non-small cell lung cancer
histology: squamous cell carcinoma
survival: long
registry year: 1998
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from 2-10 frozen tissue sections (10mm) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) and the RNeasy Mini Kit (Qiagen), respectively.
|
| 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 |
PA026_human_300A_070828
Hybridized to 250K_Nsp
|
| Data processing |
Copy number normalization, to produce log(2) ratios, was performed using the Copy Number Analysis Tool (CNAT) 4.0.1. The reference set was 82 normal samples of Caucasian origin, analyzed at the Uppsala Array Platform. Subsequent copy number analyses and group comparisons were performed using the software BioDiscovery Nexus Copy Number 3.0 and the built-in Rank Segmentation algorithm, for estimating copy numbers and segmenting each interval.
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
Jan 11, 2016 |
| Contact name |
Anders Isaksson |
| E-mail(s) |
[email protected]
|
| Organization name |
Uppsala University
|
| Street address |
Akademiska sjukhuset ing61 3tr
|
| City |
Uppsala |
| ZIP/Postal code |
75185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL3718 |
| Series (2) |
| GSE28572 |
Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer (copy number data) |
| GSE28582 |
Gene Copy Number Aberrations are Associated with Survival in Histological Subgroups of Non-Small Cell Lung Cancer |
|
| Relations |
| Reanalyzed by |
GSM2036842 |
