|
| Status |
Public on Mar 01, 2013 |
| Title |
Head and neck squamous cell carcinoma HN156 Agilent 4x44K |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Head and neck squamous cell carcinoma HN156
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Tumor
age: 48
race: African American
gender: Male
smoking packyears: 10
alcohol use: Heavy
differentiation: Moderate
tumor site: Hypopharynx
Stage: IVb
tumor status: T3
node status: N3
treatment: Concurrent Chemoradiation
hpv status: HPV-
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.
|
| |
|
| Channel 2 |
| Source name |
Stratagene Human Universal RNA Reference
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Stratagene Human Universal RNA Reference
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed as per the instructions in the Agilent Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling manual.
|
| Scan protocol |
Scanned on an Agilent High Resolution Model B scanner that has been upgraded to Model C.
Images were quantified using Agilent Feature Extraction software.
|
| Description |
Stratagene Human Universal RNA Reference
|
| Data processing |
The normexp background correction and loess normalization procedures were applied to the probe-level data using the limma R package. Normalized log2 ratios (test/reference) were then computed.
|
| |
|
| Submission date |
Jul 16, 2012 |
| Last update date |
Mar 01, 2013 |
| Contact name |
Vonn Walter |
| E-mail(s) |
[email protected]
|
| Phone |
919 323-5579
|
| Organization name |
Lineberger Comprehensive Cancer Center
|
| Lab |
Neil Hayes Lab
|
| Street address |
CB#7295, School of Medicine
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7295 |
| Country |
USA |
| |
|
| Platform ID |
GPL9053 |
| Series (2) |
| GSE39366 |
Molecular Subtypes in Head and Neck Cancer [expression] |
| GSE39368 |
Molecular Subtypes in Head and Neck Cancer |
|
