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Sample GSM465102 Query DataSets for GSM465102
Status Public on Jan 31, 2011
Title 5Aza-dC and TSA treated MDA2b Flip
Sample type RNA
 
Channel 1
Source name MDA2b_Treated_Cy3(flip)
Organism Homo sapiens
Characteristics cell line: MDA2b
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
 
Channel 2
Source name MDA2b_Mock_Cy5(flip)
Organism Homo sapiens
Characteristics strain: MDA2b
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
 
 
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 -0.87551211
2 -0.543128682
3 0.202308805
4 -0.171653485
5 -0.818364606
6 -0.492486341
7 -0.111806872
8 0.01711686
9 1.677123897
10 0.111397925
11 -0.154130694
12 0.024349548
13 0.017831067
14 -0.89794703
15 1.642337348
16 0.334201724
17 -0.433878544
18 -0.307063564
19 0.617314869
20 -0.488629686

Total number of rows: 15552

Table truncated, full table size 263 Kbytes.




Supplementary file Size Download File type/resource
GSM465102_MDA2b_Mock_Cy5_flip_.xls.gz 1.9 Mb (ftp)(http) XLS
GSM465102_MDA2b_Treated_Cy3_flip_.xls.gz 2.0 Mb (ftp)(http) XLS
Processed data included within Sample table

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