|
| Status |
Public on Oct 10, 2012 |
| Title |
HNSCC_primary_9004616 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
HNSCC_primary_9004616
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
tissue: head-neck
tumor type: HNSCC
age: 79
location: oropharynx
ct: 2
cn (clinical n-status = lymph node metastasis status): 1
pt: 2
pn (pathological n-status = lymph node metastasis status): 1
grade: 2
hpv: 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample reference protocol: A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.
|
| Label |
Cy3
|
| Label protocol |
Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf] Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70
|
| |
|
| Channel 2 |
| Source name |
UHR
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Stratagene Universal human reference cell line (UHR)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample reference protocol: A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.
|
| Label |
Cy5
|
| Label protocol |
Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf] Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70
|
| |
|
| |
| Hybridization protocol |
Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner
|
| Data processing |
Background subtracted data for the Cy5 (reference) and Cy3 (sample) channel were obtained using Agilent Feature Extraction software (version 9.5) based on MedianSignal calls. Lowess-normalization.
|
| |
|
| Submission date |
Jul 26, 2011 |
| Last update date |
Oct 10, 2012 |
| Contact name |
Paul Roepman |
| Organization name |
Agendia
|
| Street address |
Science Park 406
|
| City |
Amsterdam |
| ZIP/Postal code |
1098 XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13953 |
| Series (1) |
| GSE30788 |
Validation of an expression signature for lymph node metastasis detection in oral cavity squamous cell carcinoma |
|
