|
| Status |
Public on Feb 01, 2011 |
| Title |
Oral leukoplakia LM403 |
| Sample type |
RNA |
| |
|
| Source name |
Oral leukoplakia
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: male
race: white
alcohol habits: never
smoking habits: former
age: 54
treatment arm: retinyl palmitate
histology at baseline (hyperplasia versus dysplasia): dysplasia
histology at baseline (breakdown): mild dysplasia
p63 expression: high expression
podoplanin expression: high expression
oral cancer-free survival time (years): 2.05
outcome: oral cancer development
time of biopsy: biopsy at baseline
|
| Treatment protocol |
Samples were OCT-embedded and frozen before RNA extraction
|
| Growth protocol |
Biopsies of oral leukoplakia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols.
|
| |
|
| Hybridization protocol |
Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol.
|
| Scan protocol |
Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).
|
| Description |
RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol. RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit. For all experiments, the manufacturers' protocols were strictly followed. WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively. Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol. Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).
|
| Data processing |
Raw data of microarrays were processed using quantile normalization and RMA algorithm (RMAExpress); expression values were log2 transformed
|
| |
|
| Submission date |
Jan 11, 2011 |
| Last update date |
Feb 01, 2011 |
| Contact name |
Pierre Saintigny |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Texas M.D. Anderson Cancer Center
|
| Department |
Thoracic / Head and Neck Medical Oncology
|
| Street address |
1515 Holcombe
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE26549 |
Gene Expression Profiling Predicts the Development of Oral Cancer |
|
