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Status |
Public on Feb 08, 2023 |
Title |
CSS_3 |
Sample type |
RNA |
|
|
Source name |
LNCaP prostate cancer cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: LNCaP condition: CSS
|
Growth protocol |
LNCaP cells were cultured in phenol-red free RPMI-1640 medium + 5% FBS for 72 hrs at 37°C in a humidified atmosphere containing 5% CO2. For androgen deprivation, media was then replaced by RPMI+5% CSS (charcoal stripped serum) and cultured for another 48 hrs. For androgen stimulation, media was then changed to RPMI+5% CSS + 10 nM Dihydrotestosterone (or vehicle control) and cultured for 48 hrs before harvest.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using the RNeasy Micro Kit (Qiagen #74004) according to the manufacturer’s protocol, including DNase-I treatment.
|
Label |
Cy3
|
Label protocol |
RNA was amplified and labelled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's protocol.
|
|
|
Hybridization protocol |
Cy3 labeled cRNA was hybridised onto a custom Agilent oligo micrarray 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).
|
Description |
Cells were seeded at a density of 6,000 cells/cm2 into RPMI+5% FBS and cultured for 72 hrs, followed by 48 hrs in RPMI+5% CSS (charcoal stripped serum) before control vehicle treatment with 0.02% EtOH for 48 hrs.
|
Data processing |
Differential expression was determined using the Baysian adjusted t-statistic linear model of the ‘Linear Models for Microarray Data’ (LIMMA) package in R. Data was annotated using Gencode v21 / Ensembl 77 (GRCh38).
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|
|
Submission date |
Feb 07, 2023 |
Last update date |
Feb 15, 2023 |
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 |
GPL25684 |
Series (2) |
GSE125338 |
Transcriptome changes upon androgen deprivation and DHT stimulation in LNCaP cells |
GSE125341 |
Transcriptomic profile of YB-1 regulated downstream targets in LNCaP prostate cancer cells |
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