|
| Status |
Public on Jan 01, 2013 |
| Title |
DNA-HNSCC-29 |
| Sample type |
genomic |
| |
|
| Source name |
Pt 29
|
| Organism |
Homo sapiens |
| Characteristics |
sample identifier: Pt 29
sample type: tumor
disease state: HNSCC
|
| Treatment protocol |
human surgical specimens, flash frozen
|
| Growth protocol |
human HNSCC and UPPP surgical samples
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from all samples by digestion with 50 µg/mL proteinase K (Boehringer, Mannheim, Germany) in the presence of 1\% SDS at 48°C overnight, followed by phenol/chloroform extraction and ethanol precipitation.
|
| Label |
biotin
|
| Label protocol |
DNA samples were labeled following Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 User Guide and reagent from Affymetrix. Briefly, two aliqouts of 250 ng of high quality genomic DNA were subjected to Nsp I and Sty I digestion respectively. Nsp I adaptor and Sty I adpator were then ligated to the corresponding digested DNA and diluted 1:4. The resulting DNA were amplified by PCR using clonetech titanium PCR reagents and primer provided by Affymetrix. The amplified DNA were combined and purified using Agencourt AMPure XP magnetic beads, fragmented, and labeled using Terminal DNA Transferase.
|
| |
|
| Hybridization protocol |
The labeled DNA was hybridized to the Affymetrix GeneChip Genome-Wide human SNP 6.0 arrays for 17hr at 50 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated DNA. The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
|
| Scan protocol |
Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.0 (AGCC v3.0) software from Affymetrix, using the standard default settings.
|
| Description |
PHen-HNC-27218-1a-SNP6_0_(GenomeWideSNP_6).CEL
|
| Data processing |
Analysis was performed in R with CRLMM package.
The processed data file (linked as supplementary file on Series record) comprises CNV estimation by gene provided as the average of CNV calls across gene region.
|
| |
|
| Submission date |
Oct 25, 2011 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Michael F Ochs |
| Organization name |
Johns Hopkins University
|
| Department |
Oncology Biostatistics
|
| Street address |
550 North Broadway, Ste 1103
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE33229 |
Cancer Outlier Gene Profile Sets Elucidate Pathways and Patient-Specific Targets in Head and Neck Squamous Cell Carcinoma [Affymetrix SNP6] |
| GSE33232 |
Cancer Outlier Gene Profile Sets Elucidate Pathways and Patient-Specific Targets in Head and Neck Squamous Cell Carcinoma |
|
