|
| Status |
Public on Sep 11, 2018 |
| Title |
SNAI1.D0.R3 |
| Sample type |
RNA |
| |
|
| Source name |
LNCaP-iSnail, untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: prostate cancer cell line
model: inducible SNAI1
treatment: untreated
time: 0 days
|
| Treatment protocol |
LNCaP-iGFP and LNCaP-iSnail cells were either left untreated, treated with doxycycline for 5 days to stimulate expression of either GFP or Snail expression, or treated with doxycycline for 5 days and subsequently removed for 3, 5, and 20 days to repress the expression of GFP or Snail.
|
| Growth protocol |
LNCaP-iGFP and LNCaP-iSnail cells were cultured in phenol-red free RPMI-1640 medium + 5% fetal calf serum and maintained at 37°C in an atmosphere containing 5% CO2 for the duration of the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted using the Directzol kit including on-column DNase-I treatment.
|
| Label |
Cy3
|
| Label protocol |
150 ng of total RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
1650 ng of the labeled cRNA were hybridised onto a custom Agilent oligo microarray at 65⁰C for 17 hours.
|
| Scan protocol |
Arrays were scanned on an Agilent scanner (G2565CA) using the Agilent Scan Control Software (A.8.4.1) and feature extraction was performed using the Agilent Feature Extraction Software (10.7).
|
| Data processing |
A quantile between array normalization was applied and differential expression was determined using the Bayesian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R.
|
| |
|
| Submission date |
Apr 07, 2016 |
| Last update date |
Sep 11, 2018 |
| Contact name |
Colleen Nelson |
| Organization name |
Queensland University of Technology; University of British Columbia
|
| Department |
Institute of Health and Biomedical Innovation; Vancouver Prostate Centre
|
| Street address |
199 Ipswich Road
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4102 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16604 |
| Series (1) |
| GSE80042 |
A molecular portrait of epithelial-mesenchymal plasticity in prostate cancer associated with clinical outcome. |
|
