|
| Status |
Public on Sep 01, 2011 |
| Title |
OSCC tumor_OR4004 |
| Sample type |
genomic |
| |
|
| Source name |
OSCC specimens
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: tumor
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to Affymetrix SNP6.0
|
| Data processing |
We used Partek to detect copy number variation. We used birdseed algorithm for calling SNP 6.0, which is suggested standard algorithm, and birdseed is embedded in software of Genotyping Console (GTC) or Affymetrix Power Tool (APT) which all provide by affymetrix company. The reported summarized intensity are separated into A intensity and B intensity, and results in calling into AA, AB, or BB categories.
|
| |
|
| Submission date |
Nov 04, 2010 |
| Last update date |
Sep 01, 2011 |
| Contact name |
Chien-Hua Peng |
| Organization name |
Chang Gung Memorial Hospital
|
| Street address |
No. 5, Fu-Hsing ST.
|
| City |
Taoyuan |
| ZIP/Postal code |
33305 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE25103 |
Affymetrix SNP array data for oral squamous cell carcinoma |
| GSE25104 |
Expression and SNP array data for oral squamous cell carcinoma |
|
