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Sample GSM536179 Query DataSets for GSM536179
Status Public on Nov 30, 2013
Title tubo exp 2 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

Data table header descriptions
ID_REF
VALUE e2.e

Data table
ID_REF VALUE
6848511 9.95299
6864895 9.95867
6766590 4.58584
6914045 4.80604
6963197 6.38362
6766588 3.92604
6995964 11.2317
6766587 5.42166
6815739 5.8006
6766586 6.71174
7012346 5.46446
6766585 6.84763
6848505 9.49004
6766584 6.11804
6848504 9.49128
6979576 5.55621
6995960 7.13293
6766583 5.56295
6963191 7.36014
6979575 5.71848

Total number of rows: 23238

Table truncated, full table size 364 Kbytes.




Supplementary file Size Download File type/resource
GSM536179.CEL.gz 23.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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