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Series GSE41213 Query DataSets for GSE41213
Status Public on Feb 06, 2013
Title Identification of a set of miRNAs differentially expressed in transiently TIA-depleted HeLa cells by genome-wide profiling
Platform organisms Homo sapiens; Mus musculus; Rattus norvegicus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Murid gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus hominis; Betapolyomavirus macacae
Sample organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary Background: T-cell intracellular antigen (TIA) proteins function as regulators of cell homeostasis. These proteins control gene expression globally at multiple levels in response to dynamic regulatory changes and environmental stresses. Herein we identified a micro(mi)RNA signature associated to transiently TIA-depleted HeLa cells and analyzed the potential role of miRNAs combining genome-wide analysis data on mRNA and miRNA profiles.

Results: Using high-throughput miRNA expression profiling, transient depletion of TIA-proteins in HeLa cells was observed to promote significant and reproducible changes (>2-fold, FDR<0.0001) affecting to a pool of up-regulated miRNAs (miR-30b*, miR125a-3p, miR-193a-5p, miR-197_MM2, miR-203, miR-210, miR-371-5p, miR-373*, miR-483-5p, miR-492, miR-498, miR-503, miR-572, miR-586, miR-612, miR-615, miR-623, miR-625, miR-629, miR-638, miR-658, miR-663, miR-671, miR-769-3p and miR-744). Differential expression analysis of some miRNAs was validated by reverse transcription and real time PCR. By target prediction and combined analysis of the genome-wide expression profiles of the mRNAs and miRNAs identified in TIA-depleted HeLa cells, we detected concomitant connections between up-regulated miRNAs and putative and experimental targeted mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database analyses suggest that targeted mRNAs are related with biological processes associated to the regulation of DNA-dependent transcription, signal transduction and multicellular organismal development as well as with the enrichment of pathways in cancer, focal adhesion, regulation of actin cytoskeleton and MAPK and Wnt signalling pathways, respectively.

Conclusion: All this considered, these observations suggest that specific miRNAs could act as potential mediators of the epigenetic switch linking transcriptomic dynamics and cell phenotypes mediated by TIA proteins.
Overall design The analysis includes two cell types. Three biological replicates were performed per cell type and they were compared by using three dual-channel microarray hybridizations.
Contributor(s) Sánchez-Jiménez C, Carrascoso I, Barrero J, Izquierdo JM
Citation(s) 23387986
Submission date Sep 28, 2012
Last update date Apr 01, 2013
Contact name José María Izquierdo
Organization name CBM Severo Ochoa
Lab 107
Street address Campus de Cantoblanco
City Madrid
State/province Madrid
ZIP/Postal code 28049
Country Spain
Platforms (1)
GPL13273 EXIQON miRCURY™ V8.1 LNA array
Samples (3)
GSM1010907 Transiently TIA-depleted HeLa cells vs Control HeLa cells. Replicate 1
GSM1010908 Transiently TIA-depleted HeLa cells vs Control HeLa cells. Replicate 2
GSM1010909 Transiently TIA-depleted HeLa cells vs Control HeLa cells. Replicate 3
BioProject PRJNA176188

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE41213_RAW.tar 3.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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