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| Status |
Public on Jun 11, 2013 |
| Title |
Multiple platform assessment and isomir analysis of the EGF dependent microRNA-ome by microarray and deep sequencing analysis [Exiqon] |
| Platform organisms |
Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Betapolyomavirus hominis; Betapolyomavirus macacae |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
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.
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| Overall design |
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
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| Contributor(s) |
Llorens F, Hummel M, Pantano L, Pastor X, Vivancos A, Castillo E, Mattlin H, Ferrer A, Ingham M, Noguera M, Kofler R, Dohm JC, Pluvinet R, Bayés M, Himmelbauer H, del Rio JA, Martí E, Sumoy L |
| Citation(s) |
23724959 |
| Submission date |
Sep 28, 2012 |
| Last update date |
Jun 14, 2013 |
| Contact name |
Lauro Sumoy |
| E-mail(s) |
lsumoy@igtp.cat
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| Organization name |
IGTP
|
| Department |
High Content Genomics and Bioinformatics
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| Street address |
Ctra. Can Ruti, Camí de les escoles s/n
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| City |
Badalona |
| State/province |
Barcelona |
| ZIP/Postal code |
08916 |
| Country |
Spain |
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| Platforms (1) |
| GPL16118 |
miRCURY LNA microRNA Array, v. 9.2 - all organisms |
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| Samples (6)
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| GSM1011088 |
6h Control replicate 1 versus pool of controls |
| GSM1011089 |
6h Control replicate 2 versus pool of controls |
| GSM1011090 |
6h Control replicate 3 versus pool of controls |
| GSM1011091 |
6h EGF replicate 1 versus pool of controls |
| GSM1011092 |
6h EGF replicate 2 versus pool of controls |
| GSM1011093 |
6h EGF replicate 3 versus pool of controls |
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| This SubSeries is part of SuperSeries: |
| GSE41360 |
Multiple platform assessment and isomir analysis of the EGF dependent microRNA-ome by microarray and deep sequencing analysis |
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| Relations |
| BioProject |
PRJNA176713 |
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