|
Status |
Public on Dec 01, 2013 |
Title |
scrambled 48h 4 |
Sample type |
RNA |
|
|
Source name |
mouse breast cancer cell line
|
Organism |
Mus musculus |
Characteristics |
cell line: TUBO knockdown: scrambled time: 48h
|
Treatment protocol |
To obtain BALB-neuT cells silenced or overexpressing miR-135a and miR-135b, cells were plated in 6-well plates at 90% confluency and transfected 24h later using using LipofectamineTM2000 (Invitrogen Life Technologies, Carlsbad, CA) reagent, according to manufacturer’s instruction, with 200 nM of specific miRIDIAN microRNA Hairpin Inhibitor (anti-miR-135b) or Mimics (miR-135b-over)(Thermo Scientific Dharmacon). For each experiments cells were also transfected with miRIDIAN microRNA Hairpin Inhibitor or Mimics negative control (control).
|
Growth protocol |
BALB-neuT mammary cell lines were cultured in DMEM with Glutamax 1 (DMEM, Life Technologies) supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen)
|
Extracted molecule |
total RNA |
Extraction protocol |
mirVana miRNA isolation kit (Applied Biosystems, Milano, Italy)
|
Label |
biotin
|
Label protocol |
cRNA synthesis and labeling were done using Illumina RNA Amplification Kit (Ambion) following the procedure suggested by the manufacturer.
|
|
|
Hybridization protocol |
Standard Illumina hybridization protocol
|
Scan protocol |
Arrays were scanned on Illumina BeadStation 500 (Illumina, San Diego, CA)
|
Description |
scr48.4 scrambled 48h 4 a5535688004_A.AVG_Signal
|
Data processing |
Genome studio (Illumina, San Diego, CA) was used to generate raw intensity signal without normalization. Data log2 transformation and loess normalization was performed with oneChannelGUI v 1.16.0. 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
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|
|
Submission date |
Apr 28, 2011 |
Last update date |
Dec 01, 2013 |
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 |
|
|
Platform ID |
GPL6885 |
Series (1) |
GSE28949 |
miR-135b exerts metastatic activity in the ErbB2 driven mammary carcinogenesis |
|