Transcriptomics

Dataset Information

297

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


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 by small RNA-seq using Illumina 36-bp read massively parallel sequencing. Three independent experiments were performed where HeLa cells were serum deprived for 24 hours and were either left untreated or treated with EGF for 6h and harvested for RNA extraction. Thus, a total of 6 samples were analyzed, 3 controls and the 3 respective treated counterparts. These same samples were also analyzed in parallel on two different microarray platforms.

ORGANISM(S): Homo sapiens  

SUBMITTER: Robert Kofler   Raquel Pluvinet  Lorena Pantano  Franc Llorens  Ester Castillo  Jose A del Rio  Eulàlia Martí  Heidi Mattlin  Xavier Pastor  Lauro Sumoy  Juliane C Dohm  Marc Noguera  Anna Ferrer  Ana Vivancos  Matthew Ingham  Mònica Bayés  Manuela Hummel  Heinz Himmelbauer 

PROVIDER: E-GEOD-41359 | ArrayExpress | 2013-06-11

SECONDARY ACCESSION(S): SRP016004GSE41359PRJNA176714

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications


BACKGROUND: 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 in the c  ...[more]

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