|
| Status |
Public on Jun 01, 2009 |
| Title |
Cancer stroma, slide 9541, sample 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
prostate cancer-associated stroma
|
| Organism |
Homo sapiens |
| Characteristics |
grade 3 reactive stroma prostate cancer tissues
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Microarray analysis was performed using 2.5 micrograms of total RNA.
|
| Label |
Alexa Fluor 647
|
| Label protocol |
Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).
|
| |
|
| Channel 2 |
| Source name |
human, universal reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Stratagene, Universal Human Reference RNA Catalog #740000
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Microarray analysis was performed using 2.5 micrograms of total RNA.
|
| Label |
Alexa Fluor 555
|
| Label protocol |
Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).
|
| |
|
| |
| Hybridization protocol |
The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Human Genome arrays and rotating over night at 65 degC.
|
| Scan protocol |
Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).
|
| Description |
human grade 3 reactive stroma prostate cancer tissues, compared to universal reference RNA
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.
|
| |
|
| Submission date |
Jun 04, 2008 |
| Last update date |
Jan 16, 2009 |
| Contact name |
Chad Creighton |
| E-mail(s) |
creighto@bcm.tmc.edu
|
| Organization name |
Baylor College of Medicine
|
| Department |
Biostatistics, Ducan Cancer Center
|
| Street address |
One Baylor Plaza, Mail Stop: BCM305
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE11682 |
Gene expression profiles of reactive stroma in prostate cancer |
|
