|
| Status |
Public on Apr 11, 2012 |
| Title |
EAC_60T |
| Sample type |
RNA |
| |
|
| Source name |
Esophagectomy specimen with no preoperative chemoradiation therapy.
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Esophageal adenocarcinoma
age: 66
gender: M
ethnicity: Caucasian
Stage: IIA
tissue: esophagectomy specimen
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from primary tissues were isolated using Trizol reagent from Invitrogen and the RNeasy mini kit from QIAGEN following the manufacturers' instructions. Total RNA was isolated using the RNeasy mini kit from Qiagen, following the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human HG-U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
|
| Description |
Gene expression data from esophageal adenocarcinoma.
|
| Data processing |
Data was analyzed using the affy and limma Bioconductor package implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.
|
| |
|
| Submission date |
Apr 11, 2012 |
| Last update date |
Apr 11, 2012 |
| Contact name |
David G Beer |
| E-mail(s) |
dgbeer@umich.edu
|
| Phone |
734-763-0325
|
| Fax |
734-615-6033
|
| Organization name |
University of Michigan Medical School
|
| Department |
Surgery
|
| Lab |
Thoracic Surgery Cancer Biology Lab
|
| Street address |
1500 E Medical Center Dr. CCGC 6431
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (2) |
| GSE37201 |
Gene expression profiling of esophageal adenocarcinoma |
| GSE37203 |
Barrett's esophageal tissues and esophageal adenocarcinoma specimens |
|
