|
| Status |
Public on Feb 17, 2012 |
| Title |
PDCCE_FreshFrozen_CRC007 |
| Sample type |
RNA |
| |
|
| Source name |
mouse derived colorectal explant tumor, colon primary, liver metastasis, fresh frozen tissue
|
| Organism |
Homo sapiens |
| Characteristics |
primary tumor site: Colon
metastatic tumor site: Liver
|
| Treatment protocol |
PDCCE samples were treated with saline by intraperitoneal injection for 2.5 weeks.
|
| Growth protocol |
Colorectal cancer cells extracted from previously generated explants were injected subcutaneously into the flanks of JAX NOD.CB17-PrkdcSCID-J mice (four-week-old female) and measured every 2-3 days with a vernier caliper until the volume of the tumor (V = L×2W×0.52 (L = longest diameter, W = shortest diameter)) reached approximately 500 mm³. Tumors were grown for three additional weeks then were harvested and flash frozen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen PDCCE samples were sectioned at 8µm and placed onto histological slides. An initial section was stained with hematoxylin and eosin (Sigma) for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 µg of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, CA). RNA were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE), and quality was assessed by spectrophotomeric analysis on an Agilent 2100 Bioanalyzer conductor using the RNA 6000 nano assay Kit (Agilent Technologies, Santa Clara, 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).
|
| Description |
PDCCE Fresh Frozen CRC007
|
| 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 |
|
