|
| Status |
Public on Apr 11, 2012 |
| Title |
BE_03B |
| Sample type |
RNA |
| |
|
| Source name |
Esophagectomy specimen with no preoperative chemoradiation therapy.
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Barrett’s esophageal tissues
age: 70
gender: M
ethnicity: Caucasian
Stage: NA
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 U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 3000 GeneChip Scanner.
|
| Description |
Gene expression data from Barrett’s esophageal tissues.
|
| Data processing |
Data was analyzed using the affy 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 |
GPL96 |
| Series (2) |
| GSE37200 |
Gene expression profiling of Barrett’s esophageal tissues and esophageal adenocarcinoma specimens |
| GSE37203 |
Barrett's esophageal tissues and esophageal adenocarcinoma specimens |
|
