NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM465099 Query DataSets for GSM465099
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

Data table header descriptions
ID_REF
VALUE lowess normalized log ratio (treated/mock)

Data table
ID_REF VALUE
1
2
3 -0.161433024
4 0.504627408
5 -3.926542024
6 -0.733036183
7 -0.425264506
8 -0.588899374
9 -0.698039116
10 -0.638297317
11 -0.50521632
12 0.49066564
13 -0.621174808
14 -0.550465188
15 0.708947557
16 -1.671379806
17 -1.421103487
18
19
20 -0.905872728

Total number of rows: 15552

Table truncated, full table size 257 Kbytes.




Supplementary file Size Download File type/resource
GSM465099_LNCaP_Mock_Cy3.xls.gz 2.0 Mb (ftp)(http) XLS
GSM465099_LNCaP_Treated_Cy5.xls.gz 1.9 Mb (ftp)(http) XLS
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap