Unknown,Transcriptomics,Genomics,Proteomics

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Multiple platform assessment and isomir analysis of the EGF dependent microRNA-ome by microarray and deep sequencing analysis [Agilent]


ABSTRACT: We have used an integrative high content analysis approach to identify the specific miRNAs implicated in EGF signaling in HeLa cells as potential mediators of cancer mediated functions. We have used microarray and deep-sequencing technologies in order to obtain a global view of the EGF miRNA transcriptome with a robust experimental cross-validation. By applying a procedure based on Rankprod tests, we have delimited a solid set of EGF-regulated miRNAs. After validating regulated miRNAs by RT-qPCR, we have derived protein networks and biological functions from the predicted targets of the regulated miRNAs to gain insight into the potential role of miRNAs in EGF-treated cells. In addition, we have analyzed sequence heterogeneity due to editing relative to the reference sequence (isomirs) among regulated miRNAs. Time course experiment comparing HeLa gene expression in response to EGF analyzed on different microarray platforms and by digital gene expression using short read high throughput sequencing by synthesis. Three independent experiments were performed where HeLa cells were serum deprived for 24 hours and were either left untreated or treated with EGF for 6 h and harvested for RNA extraction. treated vs. untreated comparison, time course

ORGANISM(S): Homo sapiens

SUBMITTER: Lauro Sumoy 

PROVIDER: E-GEOD-41181 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications


<h4>Background</h4>Epidermal Growth Factor (EGF) plays an important function in the regulation of cell growth, proliferation, and differentiation by binding to its receptor (EGFR) and providing cancer cells with increased survival responsiveness. Signal transduction carried out by EGF has been extensively studied at both transcriptional and post-transcriptional levels. Little is known about the involvement of microRNAs (miRNAs) in the EGF signaling pathway. miRNAs have emerged as major players i  ...[more]

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