|
Status |
Public on Jan 31, 2011 |
Title |
5Aza-dC and TSA treated LNCaP |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
LNCaP_Treated_Cy5
|
Organism |
Homo sapiens |
Characteristics |
cell line: LNCaP
|
Treatment protocol |
Cells were exposed to 5Aza-dC to a final concentration of 5mM at 0, 24 and 72 hours, over two cell divisions by counting of the cells, and then, treated with TSA to a final concentration of 500nM during the 24 hours before DNA extraction. Mock (untreated) cells were cultured with the equivalent volume of PBS alone and, for the 24 hours before RNA extraction, with the equivalent volume of EtOH.
|
Growth protocol |
Four prostate cancer cell lines were grown at 37C using RPMI medium (LNCaP), F12K medium (PC3 and MDA2b) and MEM medium (DU-145).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from drug-treated and mock cultured cells using TRIZOL reagent (Invitrogen, Carlsbad, CA) and purified with the RNAeasy Mini kit (Qiagen, Valencia, CA) combined with DNase treatment.
|
Label |
Cy5
|
Label protocol |
cDNA labelled with Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ) according to the manufacturer’s instructions
|
|
|
Channel 2 |
Source name |
LNCaP_Mock_Cy3
|
Organism |
Homo sapiens |
Characteristics |
strain: LNCaP
|
Treatment protocol |
Cells were exposed to 5Aza-dC to a final concentration of 5mM at 0, 24 and 72 hours, over two cell divisions by counting of the cells, and then, treated with TSA to a final concentration of 500nM during the 24 hours before DNA extraction. Mock (untreated) cells were cultured with the equivalent volume of PBS alone and, for the 24 hours before RNA extraction, with the equivalent volume of EtOH.
|
Growth protocol |
Four prostate cancer cell lines were grown at 37C using RPMI medium (LNCaP), F12K medium (PC3 and MDA2b) and MEM medium (DU-145).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from drug-treated and mock cultured cells using TRIZOL reagent (Invitrogen, Carlsbad, CA) and purified with the RNAeasy Mini kit (Qiagen, Valencia, CA) combined with DNase treatment.
|
Label |
Cy3
|
Label protocol |
cDNA labelled with Cy3 and Cy5 (Amersham Biosciences, Piscataway, NJ) according to the manufacturer’s instructions
|
|
|
|
Hybridization protocol |
Labelled cDNA hybridised according to the manufacturer’s instructions
|
Scan protocol |
The hybridized slides were scanned using a GMS 428 Scanner (Affymetrix, Santa Clara, CA)
|
Description |
n/a
|
Data processing |
Image analysis was performed using the ImaGene software (BioDiscovery, Inc, El Segundo, CA). The spots were identified using an optimized segmentation algorithm. Normalization and background correction were performed using LOWESS with a width of 0.7 and local background correction.
|
|
|
Submission date |
Oct 23, 2009 |
Last update date |
Jan 31, 2011 |
Contact name |
Ilsiya Ibragimova |
E-mail(s) |
ilsiya.ibragimova@fccc.edu
|
Organization name |
Fox Chase Cancer Center
|
Department |
ICR
|
Lab |
Paul Cairns
|
Street address |
333 Cottman ave, w350
|
City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19111 |
Country |
USA |
|
|
Platform ID |
GPL9452 |
Series (1) |
GSE18573 |
Global Reactivation of Epigenetically Silenced Genes in Prostate Cancer |
|