|
| Status |
Public on Oct 07, 2011 |
| Title |
Surgical sample OPE049 |
| Sample type |
RNA |
| |
|
| Source name |
Esophagus, cancerous portion, surgical
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: esophageal cancer
tissue: cancerous portion of esophagus
sample type: surgical
patient identifier: 49
|
| Treatment protocol |
All surgical samples were obtained from esophageal cancer patients without neoadjuvant therapy, and all biopsy samples were obtained before treatment. For the surgical samples, trained pathologists carefully excised bulk tissue samples from the main tumor, leaving a clear margin from the surrounding normal tissue. Surgical and biopsy samples were immediately frozen at -80ﾟC until use. Frozen samples were placed in the ISOGEN solution (Nippon Gene, Toyama, Japan) and homogenized before total RNA extraction.
|
| Growth protocol |
All esophageal cancer tissues and non-cancerous tissues were provided by the Central Hospital or East Hospital at the National Cancer Center after obtaining written informed consent from each patient and approval by the Center’s Ethics Committee.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ISOGEN extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 100 ng total RNA by the two-cycle cDNA synthesis system. The procedure was according to the standard Affymetrix protocol (Section 2: Eukaryotic sample and array processing).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45ﾟC on the GeneChip Human Genome Array U95Av2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.
|
| Description |
OPE049
Gene expression data from surgical sample of esophageal cancer.
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using default settings by Expression Console ver 1.1.
|
| |
|
| Submission date |
Oct 07, 2011 |
| Last update date |
Oct 07, 2011 |
| Contact name |
Hiroki Sasaki |
| Organization name |
National Cancer Center Reseach Institute
|
| Street address |
Tukiji5-1-1
|
| City |
Chuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
104-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE22954 |
Artificially induced epithelial-mesenchymal transition in surgical subjects: its implications in clinical and basic cancer research |
| GSE32701 |
Individual aiEMT in surgical samples of esophageal cancer patients |
|
