|
| Status |
Public on Nov 12, 2014 |
| Title |
LNCaP+HPS-19I co-culture, no TGF-beta but with SD208 (36023_2) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
LNCaP prostate cancer cells and HPS-19I cells
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: LNCaP+HPS-19I co-culture, no TGF-beta but with SD208
|
| Growth protocol |
HPS19I cells were grown to mostly confluence in T75 flasks. 5X105 of LNCaP-HA-TGF-β1(a) cells or LNCaP-Ctrl cells were then plated on top of the HPS19I cells. The co-cultures were maintained in RPMI1640 supplemented with 0.2% FBS and subjected to treatments with 400 nM of SD208 or vehicle control for 6 days.
|
| 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 |
Stratagene, Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Stratagene, Universal Human Reference RNA
|
| Growth protocol |
HPS19I cells were grown to mostly confluence in T75 flasks. 5X105 of LNCaP-HA-TGF-β1(a) cells or LNCaP-Ctrl cells were then plated on top of the HPS19I cells. The co-cultures were maintained in RPMI1640 supplemented with 0.2% FBS and subjected to treatments with 400 nM of SD208 or vehicle control for 6 days.
|
| 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 |
HPS_19I LNCaP_pBMN +SD208 36023_2
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used. Combat used for batch effect correction (PMID:16632515).
|
| |
|
| Submission date |
Oct 23, 2013 |
| Last update date |
Nov 12, 2014 |
| Contact name |
Chad Creighton |
| E-mail(s) |
[email protected]
|
| 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 (2) |
| GSE51617 |
Expression profiling of co-cultures of prostate cancer cells and stroma cells, with or without TGF-beta signaling |
| GSE51624 |
Co-cultures of prostate cancer cells and stroma cells, with or without TGF-beta signaling |
|
