|
| Status |
Public on Feb 17, 2012 |
| Title |
HumanTumor_FreshFrozen_CRC039 |
| Sample type |
RNA |
| |
|
| Source name |
human tumor, colon primary, liver metastasis, fresh frozen tissue
|
| Organism |
Homo sapiens |
| Characteristics |
primary tumor site: Colon
metastatic tumor site: Liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 gene expression data were RMA-estimated using the R statistical platform with the Bioconductor affymetrix package.
|
| |
|
| Submission date |
Apr 18, 2011 |
| Last update date |
May 14, 2012 |
| Contact name |
David Hsu |
| E-mail(s) |
hsu00018@dm.duke.edu
|
| Phone |
919-684-1739
|
| Fax |
919-668-4777
|
| Organization name |
Duke University
|
| Department |
Institute for Genome Sciences and Policy
|
| Street address |
Rm 2167 CIEMAS Bldg, 101 Science Dr.
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE28691 |
Characterization of an Oxaliplatin Sensitivity Predictor in a preclinical Murine Model of Colorectal Cancer |
|
