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E-GEOD-66279 - Effect of decitabine, carboplatin and their combination on gene expression in the YB5 colon cancer cell line

Status
Released on 8 September 2015, last updated on 12 September 2015
Organism
Homo sapiens
Samples (6)
Array (1)
Protocols (7)
Description
YB5 cell line is a clonal derivative of the SW48 colon cancer cell line that contains a single copy of a green fluorescent protein (GFP) reporter silenced by CpG methylation at its CMV promoter. We treated the YB5 cells with decitabine (5-aza-2’-deoxycytidine), carboplatin and the combination of decitabine plus carboplatin and analyzed the effects of the drugs on gene expression. YB5 cells in the early log phase of growth were seeded at 3.5 million in 20 ml of culture medium in 10 cm diameter tissue culture plates at day 0. The cells were treated with 20 microliters of decitabine (final concentration 25 nM), carboplatin (final concentration 20 uM) or both at days 1, 2, 3 and 4. Control cells were treated with 20 microliters of diluent (DMSO). The cells were harvested at day 6. Total RNA was extracted by TRIZOL, labeled with Cy5 (control cells) or Cy3 (treated cells) and hybridized on Agilent Whole Genome Array (G4112F). Raw data from the Agilent scanner were loess normalized using Bioconductor packages limma and agilp.
Experiment type
transcription profiling by array 
Contacts
Jaroslav Jelinek, Jean-Pierre J Issa, Jiali Si
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-66279.idf.txt
Sample and data relationshipE-GEOD-66279.sdrf.txt
Raw data (1)E-GEOD-66279.raw.1.zip
Processed data (1)E-GEOD-66279.processed.1.zip
Array designA-AGIL-28.adf.txt
Links