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Sample GSM7032056 Query DataSets for GSM7032056
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).
 
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

Data table header descriptions
ID_REF
VALUE quantile normalised log2 transformed probe intensities

Data table
ID_REF VALUE
A_14_P100100 5.024384159
A_14_P100208 12.53094938
A_14_P100325 5.062168821
A_14_P100335 8.147436219
A_14_P100337 4.788495895
A_14_P100385 5.778973121
A_14_P100389 5.134892985
A_14_P100419 4.722962735
A_14_P100529 4.745139526
A_14_P100533 4.919946748
A_14_P100535 8.403012024
A_14_P100560 5.742692205
A_14_P100627 5.751239725
A_14_P100804 8.578458467
A_14_P100819 6.02639769
A_14_P100933 6.454205809
A_14_P100966 5.062168821
A_14_P100985 4.764570056
A_14_P101047 4.788495895
A_14_P101187 13.18796356

Total number of rows: 175281

Table truncated, full table size 3703 Kbytes.




Supplementary file Size Download File type/resource
GSM7032056_US81603235_253203410072_S01_GE1_107_Sep09_1_1.txt.gz 8.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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