|
| Status |
Public on Feb 28, 2015 |
| Title |
Oral cancer patient, Male 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Freshly operated oral cancer tissue of a male
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: oral cancer
tissue: Freshly operated oral cancer tissue
age: 47
Stage: 4
tobacco habit: Yes
node metastasis: Negative
histology: WDSCC
gender: Male
sample collection date: 2007
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was isolated from 5-10ml blood or from fresh operated tissue samples by QIAGEN blood DNA isolation kit or by the conventional phenol-chloroform method followed by ethanol precepitation (Sambrook, 1989), respectively.
|
| Label |
Cy5
|
| Label protocol |
DNA was lebelled by Agilent Genomic DNA Labeling Kit PLUS as per manufacture's instructions.
|
| |
|
| Channel 2 |
| Source name |
Blood of normal male
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: normal control
tissue: blood
age: 50
gender: male
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was isolated from 5-10ml blood or from fresh operated tissue samples by QIAGEN blood DNA isolation kit or by the conventional phenol-chloroform method followed by ethanol precepitation (Sambrook, 1989), respectively.
|
| Label |
Cy3
|
| Label protocol |
DNA was lebelled by Agilent Genomic DNA Labeling Kit PLUS as per manufacture's instructions.
|
| |
|
| |
| Hybridization protocol |
Hybridization was done by Agilent’s In situ Hybridzation kit 5188-5220 as per manufacture's instructions.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Description |
1 vs. N(M)
|
| Data processing |
Agilent Feature Extraction Software was used to extract raw data from scanned images and data analysis is done using DNA Analytics software form Agilent Technologies using ADM2 algorithm. minAvgAbsLogRatio = 0.45, threshold=6.0, fuzzy zero=on
|
| |
|
| Submission date |
Jan 16, 2014 |
| Last update date |
Feb 28, 2015 |
| Contact name |
Hamid Band |
| E-mail(s) |
hband@unmc.edu
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Eppley
|
| Street address |
42nd and Emile
|
| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68198 |
| Country |
USA |
| |
|
| Platform ID |
GPL18173 |
| Series (1) |
| GSE54165 |
Custom array CGH of Oral Squamous Cell Cancer |
|
