|
| Status |
Public on Mar 04, 2009 |
| Title |
gastric cancer patient20 with relapse free in retrospective phase |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
15 Total RNAs mixture from normal gastric mucosa labeled with Cyanine-3 (green).
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: mixture of normal gastric mucosa
|
| Treatment protocol |
Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)
|
| |
|
| Channel 2 |
| Source name |
gastric cancer patient with relapse free in retrospective phase
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary gastric cancer
phenotype: gastric cancer with no recurrence
|
| Treatment protocol |
Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.
|
| Label |
Cy5
|
| Label protocol |
Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)
|
| |
|
| |
| Hybridization protocol |
Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)
|
| Scan protocol |
ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).
|
| Description |
Retro_RF20
|
| Data processing |
In each sample, intensity values for both channels (Cy5 and Cy3) were independently transformed using a quantile equalization method, yielding pairs of normalized values of non-exponential scale. We enforced the normalized values to follow an independent hypothetical standard normal distribution, keeping only the rank within a sample and a chennel. The abundance of transcription for each probe was then defined by subtracting the value of Cy5 from that of Cy3, which are free from dye-sensor bias and can be treated just like the log ratio of Cy5 and Cy3.
|
| |
|
| Submission date |
Mar 03, 2009 |
| Last update date |
Mar 03, 2009 |
| Contact name |
ATSUSHI TAKENO |
| E-mail(s) |
atakeno@gesurg.med.osaka-u.ac.jp
|
| Phone |
+81668793251
|
| Fax |
+81668793259
|
| Organization name |
Osaka university
|
| Department |
Surgery
|
| Street address |
2-2, Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1291 |
| Series (1) |
| GSE15081 |
Gene expression profile prospectively predicts peritoneal relapse after curative surgery of gastric cancer |
|
