|
| Status |
Public on Nov 25, 2013 |
| Title |
PC-3_Icilin, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Prostate cancer cell line PC-3, icilin
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC-3
cell type: androgen-independent prostate carcinoma cell line
treatment: icilin
|
| Treatment protocol |
Compounds were dissolved in ethanol as a vehicle at 0.1% working concentration and treated in PC-3 cells. Vehicle-treated PC-3 cells were used as a control.
|
| Growth protocol |
The cells were maintained under DMEM medium containing 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the cells and processed according to the manufacturer's guideline (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol was performed using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 1.0 ST arrays. The hybridized probe arrays were stained and washed with the GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G (Affymetrix) at 570 nm.
|
| Description |
icilin effect on gene expression profile in PC-3 cells.
|
| Data processing |
Raw data were normalized using the Single Channel Array Normalization (Piccolo et al. 2012, PMID: 22959562) method, which is implemented as a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). As part of the normalization process, a custom chip-definition (CDF) file from the BrainArray resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated probes. Microarray probes to 11,931 genes.
|
| |
|
| Submission date |
Mar 27, 2013 |
| Last update date |
Mar 12, 2020 |
| Contact name |
Ju-Hong Jeon |
| E-mail(s) |
[email protected]
|
| Organization name |
Seoul National University College of Medicine
|
| Department |
Department of Physiology and Biomedical Sciences
|
| Lab |
Smooth muscle lab
|
| Street address |
28 Yongon-Dong, Chongno-Gu
|
| City |
Seoul |
| State/province |
Seoul |
| ZIP/Postal code |
110-799 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL15034 |
| Series (1) |
| GSE45567 |
The transcriptional network for cell cycle regulation in prostate cancer |
|
