NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE28949 Query DataSets for GSE28949
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
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.
 
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.
 
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
 
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (16)
GSM717375 scrambled 48h 4
GSM717376 scrambled 48h 5
GSM717377 scrambled 48h 6
Relations
BioProject PRJNA140431

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

Supplementary file Size Download File type/resource
GSE28949_RAW.tar 3.1 Mb (http)(custom) TAR
GSE28949_non-normalized.txt.gz 1023.3 Kb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap