|
| Status |
Public on Jul 02, 2009 |
| Title |
stageII colorectal cancer patient3 with distant recurrence in discovery phase |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
40 Total RNA mixture from normal colorectal mucosa labeled with Cyanine-3 (green).
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: mixture of normal colorectal mucosa
|
| Treatment protocol |
no treatment
|
| 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 |
Total RNA from primary colorectal cancer of stageII patient with distant recurrence labeled with Cyanine-5 (red).
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: stageII colorectal cancer with distant recurrence
|
| Treatment protocol |
no treatment
|
| Extracted molecule |
total RNA |
| Extraction 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.
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 |
no additional information
|
| Data processing |
In each sample, the Cy5/Cy3 ratio values were log-transformed and global equalization to remove a deviation of the signal intensity between whole Cy3- and Cy5-fluorescence was performed by subtracting a median of all log (Cy5/Cy3) values from each log (Cy5/Cy3) value. Genes with missing values in more than 10% of samples were excluded from further analysis.
|
| |
|
| Submission date |
Jul 08, 2008 |
| Last update date |
Jul 08, 2008 |
| Contact name |
masakazu miyake |
| E-mail(s) |
m.masakazu@k4.dion.ne.jp
|
| Phone |
+81-6-6879-3251
|
| Fax |
+81-6-6879-3259
|
| Organization name |
Graduate School of Medicine, Osaka University
|
| Department |
Gastroenterological Surgery
|
| Street address |
Yamadaoka 2-2
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1291 |
| Series (1) |
| GSE12032 |
Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence |
|
