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| Status |
Public on Dec 01, 2013 |
| Title |
miR-135b exerts metastatic activity in the ErbB2 driven mammary carcinogenesis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
In view of the roles played by miRNAs in cancer progression, we performed a microarray analysis aimed at identifying miR-135b target genes in breast cancer cells. Detection of transcripts affected by silencing of mir-135b was done using a time course at 24, 48 and 72 h both transfecting cell with mir-135b specific miRIDIAN microRNA Hairpin Inhibitor or miRIDIAN microRNA Hairpin Inhibitor negative control. Each experimental condition was repeated three times and analysed on on MOUSEREF-8 V2 Illumina bead chips. Genome studio was used to generate raw intensity signal without normalization. Data log2 transformation and loess normalization was performed with oneChannelGUI. Data were filtered using an IQR filter (i.e. only genes characterized by an IQR > 0.25, were retained for further analysis). Detection of differentially expressed transcripts was also performed with oneChannelGUI, using masigpro package with default parameters. Data were visualized by hierarchical clustering, as log2 ratio between anti-miR135b and the negative control using TMEV software. The subset of transcripts characterized by an increase in expression as consequence of a reduction of expression of miR135b were selected. MicroRNA target data for mir135b were retrieved from miranda database (microRNAsmiranda.mouse_predictions_S_C_aug2010.txt, http://www.microrna.org/microrna/home.do). Miranda data and transcripts increasing their expression upon silencing of miR135b were intersected to find the genes in common.
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| Overall design |
Detection of transcripts affected by silencing of mir-135b was done using a time course at 24, 48 and 72 h both transfecting cell with mir-135b specific miRIDIAN microRNA Hairpin Inhibitor or miRIDIAN microRNA Hairpin Inhibitor negative control.
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| Contributor(s) |
Quaglino E, Arigoni M, Ercole E, Riccardo F, Cantarella D, Orso F, Forni G, Cavallo F, Calogero RA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 28, 2011 |
| Last update date |
Jun 14, 2018 |
| Contact name |
Raffaele A Calogero |
| E-mail(s) |
raffaele.calogero@unito.it
|
| Phone |
++39 0116706454
|
| Organization name |
University of Torino
|
| Department |
Molecular Biotechnology Center
|
| Lab |
Bioinformatics and Genomics Unit
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
To |
| ZIP/Postal code |
10126 |
| Country |
Italy |
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| Platforms (1) |
| GPL6885 |
Illumina MouseRef-8 v2.0 expression beadchip |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA140431 |
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