|
Status |
Public on Mar 07, 2013 |
Title |
HPV-negative OSCC #32 |
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: 50-59 Sex: M vital: Alive fu time: 80.16 treatment: multii-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
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|
|
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.
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|
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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 |
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