|
| Status |
Public on Nov 30, 2013 |
| Title |
tubo exp 3 epithelial bulk |
| Sample type |
RNA |
| |
|
| Source name |
adherent TuBo epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
cell line: TuBo
cell type: adherent TuBo epithelial cells
|
| Growth protocol |
The adherent TuBo epithelial cells were generated from a mammary carcinoma arising in a BALB/c mouse female transgenic for the activated rat ErbB2 oncogene (BALB-neuT) [Rovero et al. J Immunol, 2000. 165:5133-42] and were cultured in DMEM supplemented with 20% FCS (GIBCO, Grand Island, NY).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mirvana kit (Ambion)
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized using Affymetrix kit starting from 100 ng of total RNA and following the procedure suggested by the manufacturer.
|
| |
|
| Hybridization protocol |
Affimetrix GeneChip® Exon 1.0 ST hybridization, washing, and staining were also done, as suggested by the manufacturer.
|
| Scan protocol |
Arrays were scanned on Affymetrix Scanner 3000 7G as suggested by manufaturer
|
| Description |
Exon-level analysis: detecting the presence of isoforms specific of CSC derived by TuBo cell line. The analysis was done comparing TuBo cells grown in adherent conditions with respect to mammospheres derived by TuBo cells grown under no-adherent conditions.
|
| Data processing |
GeneChip® Exon 1.0 ST arrays data quality control was done using Affymetrix Expression Console (www.affymetrix.com). Probe average intensity signal was calculated using oneChannelGUI package [Sanges et al. Bioinformatics. 2007, 24, 3406-8]. Probe set intensities were calculated using the RMA algorithm and normalized by the sketch quantile method [Irizarry et al. Biostatistics 2003, 4:249-264.]. Putative splicing events were detected using MiDAS (www.affymetrix.com) 2-way anova implemented in oneChannelGUI. Exons characterized by a p-value ≤ 0.05 in all three comparison (E vs P1, E vs P2 and E vs P3) were manually inspected using oneChannelGUI visualization tools.
|
| |
|
| Submission date |
Apr 22, 2010 |
| Last update date |
Nov 30, 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 |
GPL6096 |
| Series (2) |
| GSE21475 |
From mouse to humans: detecting preventing vaccination targets associated to breast cancer stem cells. Exon-level analysis |
| GSE21486 |
From mouse to humans: detecting preventing vaccination targets associated to breast cancer stem cells |
|
