|
| Status |
Public on Apr 25, 2011 |
| Title |
colon carcinoma_MS98 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
pool of individual tumors
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the adipose samples by Qiagen RNeasy spin columns with DNAse treatment. 2 µg of each sample was precipitated in ethanol and re-suspended in 14 µl of water. Globin mitigation performed using Ambion's GLOBINclear kit (cat# AM1
|
| Label |
Cy3
|
| Label protocol |
Custom automated version of the aminoallyl MessageAmp II kit from Ambion
|
| |
|
| Channel 2 |
| Source name |
colon carcinoma_MS98
|
| Organism |
Homo sapiens |
| Characteristics |
Stage: 2
overall survival (years): 8.23
overall survival censor (1-censored,0-non-censored): 1
metastasis (1-yes, 0-no): 0
time to metastasis (years): N/A
time to recurrence (years): 8.23
age at diagnosis: 68
tumor location: ascend
duke's stage: B
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the adipose samples by Qiagen RNeasy spin columns with DNAse treatment. 2 µg of each sample was precipitated in ethanol and re-suspended in 14 µl of water. Globin mitigation performed using Ambion's GLOBINclear kit (cat# AM1
|
| Label |
Cy5
|
| Label protocol |
Custom automated version of the aminoallyl MessageAmp II kit from Ambion
|
| |
|
| |
| Hybridization protocol |
Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybrid
|
| Scan protocol |
Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction s
|
| Description |
human colorectal tumor RNA
|
| Data processing |
Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the
|
| |
|
| Submission date |
Apr 19, 2011 |
| Last update date |
Apr 25, 2011 |
| Contact name |
Michael Nebozhyn |
| Organization name |
Merck, Inc
|
| Department |
GpGx/Computational System biology
|
| Street address |
Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4
|
| City |
West Point |
| State/province |
PA |
| ZIP/Postal code |
19486 |
| Country |
USA |
| |
|
| Platform ID |
GPL13425 |
| Series (2) |
| GSE28722 |
EMT is the dominant program in human colon cancer (Agilent) |
| GSE28814 |
EMT is the dominant program in human colon cancer |
|
