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E-GEOD-53187 - Transcriptome and translatome profiling of CPX 24h effects in neuroblastoma cells CHP134

Status
Released on 1 June 2016, last updated on 4 June 2016
Organism
Homo sapiens
Samples (12)
Array (1)
Protocols (9)
Description
Neuroblastoma (NB) is the most frequent extracranial solid tumour of childhood. Clinical courses are highly variable, ranging from spontaneous regression/maturation to rapid progression despite intensive multimodal therapy. The estimation of 5-year event free survival in high-risk patients of only about 40 % stresses an importance of novel therapeutic strategies. A number of iron chelators have demonstrated marked in vitro and in vivo anti-tumor activity and are currently being developed as novel anti-cancer agents. Therefore, the potential antitumor effect of iron chelators in NB cancer was investigated. Among the compounds tested, ciclopirox olamine (CPX) was shown to be one of the most effective intracellular iron chelators in NB cells. To unveil the molecular mechanisms underlying the effects of CPX on viability of NB cells, microarray analysis was performed in CHP134 control cells and cells treated with 5 µM CPX for 24 hours. Inclusion of both total RNA (reflecting transcriptional status of the cells) and polysomal RNA (approximating the proteomic representation of the cells) provided us with a deeper understanding of changes in the cells upon CPX treatment. Keywords: ciclopirox olamine, iron chelator, neuroblastoma, translatome profiling, transcriptome profiling, polysomal profiling, polysomal RNA, translational control, translational profiling, polysome profiling Microarray analysis was performed to enable a comprehensive view of the changes in the transcriptional and translational status of the cells in response to the treatment with an iron chelator CPX. Polysomal RNA and total RNA were isolated from vehicle-treated CHP134 cells and CHP134 cells treated with 5 µM CPX for 24 hours. Each condition is represented by three biological replicates, i.e. the experiment was repeated starting each time from cells seeding yielding an independent RNA sample. In total, 12 samples corresponding to 4 conditions were subjected to microarray analysis.
Experiment type
transcription profiling by array 
Contacts
Alessandro Quattrone, Toma Tebaldi, Valentina Adami, Valentina Greco, Viktoryia Sidarovich
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-53187.idf.txt
Sample and data relationshipE-GEOD-53187.sdrf.txt
Raw data (1)E-GEOD-53187.raw.1.zip
Processed data (1)E-GEOD-53187.processed.1.zip
Array designA-AGIL-28.adf.txt
Links