|
| Status |
Public on Dec 01, 2013 |
| Title |
scrambled 24h 2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse breast cancer cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: TUBO
knockdown: scrambled
time: 24h
|
| 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 |
scr24.2
scrambled 24h 2
g5535688004_G.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
|
| |
|
| 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 |
|
