|
| Status |
Public on Mar 07, 2013 |
| Title |
HPV-negative OSCC #29 |
| Sample type |
RNA |
| |
|
| Source name |
HPV-negative OSCC patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: HPV-negative oral squamous cell carcinoma (OSCC)
tumor stage: III/IV
age: 40-49
Sex: F
vital: Dead-oral ca
fu time: 15.31
treatment: uni-modality
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA and DNA from each specimen were simultaneously extracted using TRIzol method.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA were prepared from 1.0 to 2.5 ug of total RNA using the GeneChip Expression 3'-Amplification Reagents Kit per manufacturer's protocol
|
| |
|
| Hybridization protocol |
The cRNA was hybridized to an Affymetrix U133 2.0 Plus GeneChip arrays per Affymetrix protocols
|
| Scan protocol |
GeneChip arrays were scanned using an Affymetrix GeneChip arrays Scanner 3000 7G in the Fred Hutchinson Cancer Research Center's Genomics Shared Resources
|
| Data processing |
We used gcRMA algorithm from Bioconductor to extract gene expression values and perform normalization. The data were analyzed using a regression-based, estimating equations approach implemented in GenePlus software. The hierarchical clustering was performed using Affymetrix GeneSpring software GX 7.3.1.
|
| |
|
| Submission date |
Oct 16, 2012 |
| Last update date |
Mar 07, 2013 |
| Contact name |
Chu Chen |
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
PHS
|
| Street address |
1100 Fairview Ave. N, PO Box 19024, M/S M5-C800
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE41613 |
A 13-gene signature prognostic of HPV-negative OSCC: discovery and external validation |
|
