|
| Status |
Public on Dec 31, 2016 |
| Title |
HumanTumor_FreshFrozen_PRI_DH007 |
| Sample type |
RNA |
| |
|
| Source name |
human tumor, colorectal primary, fresh frozen tissue
|
| Organism |
Homo sapiens |
| Characteristics |
primary tumor site: colorectal
metastatic tumor site: NA
molecular subgroup: MSCC 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human tumors were flash frozen in OCT at time of surgical resection. An initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
|
| Data processing |
The data were analyzed using the R statistical platform with the Bioconductor affymetrix package [R version 2.13.1 (2011-07-08) and Bioconductor version 2.9].
|
| |
|
| Submission date |
Oct 12, 2012 |
| Last update date |
Dec 31, 2016 |
| Contact name |
David Hsu |
| Organization name |
Duke University
|
| Department |
Medical Oncology
|
| Street address |
905 S. LaSalle St. Rm 3008
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE41568 |
A Molecular Profile of Colorectal Cancer to Guide Therapy [PDCCEs] |
| GSE51244 |
A Molecular Profile of Colorectal Cancer to Guide Therapy |
|
