|
| Status |
Public on Oct 18, 2013 |
| Title |
esophageal squamous epithelium_12 |
| Sample type |
RNA |
| |
|
| Source name |
esophageal squamous epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: esophageal squamous epithelium
|
| Treatment protocol |
Laser capture microdissection was performed for all BE and EAC cases. Desired tumor cell or BE areas were selected, cut and collected for total RNA isolation.
|
| Growth protocol |
Biopsies were taken by upper gastrointestinal endoscopy with biopsy sampling. All samples were snap-frozen in liquid nitrogen and stored at -80°C. Each specimen included in this study was histopathologically approved by Dr. Vieth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (GeneChip Eukaryotic Target labeling Assays for Expression Analysis - Two Cycle labeling Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner 3000. Images were processed using GCOS.
|
| Data processing |
CEL data files were imported in GeneSpring GX 10.0.2 software (Agilent Technologies, Santa Clara, USA) and pre-processed using the GC-RMA algorithm. Statistical analysis for differentially expressed genes was performed using Welch-test.
|
| |
|
| Submission date |
Jan 26, 2011 |
| Last update date |
Oct 18, 2013 |
| Contact name |
Qing Wang |
| E-mail(s) |
wang.qing@mdc-berlin.de
|
| Phone |
+493094063798
|
| Fax |
+493094062846
|
| Organization name |
Charite-Berlin
|
| Department |
Surgical Oncology
|
| Street address |
Robert Rössle Str. 10
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE26886 |
Gene expression profiling of Barrett's esophagus, adenocarcinoma, esophageal squamous epithelium and squamous cell carcinoma |
|
