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Sample GSM536355 Query DataSets for GSM536355
Status Public on Nov 30, 2013
Title tubo exp 5 mammospheres p3
Sample type RNA
 
Source name non-adherent TuBo-derived mammospheres p3
Organism Mus musculus
Characteristics strain: BALB/c
cell line: TuBo
cell type: non-adherent TuBo-derived mammospheres p3
Growth protocol Single TuBo cells were plated in ultra low attachment flasks (Corning Life Sciences, Chorges, France) at 6 x 104 viable cells/ml in serum-free DMEM-F12 medium (Cambrex BioScience, Venviers, Belgium) supplemented with 20 ng/ml basic fibroblast growth factor (bFGF), 20 ng/ml epidermal growth factor (EGF), 5 μg/ml insulin, and 0.4% bovine serum albumin (BSA), all from Sigma-Aldrich (St. Louis, MO). Nonadherent spherical clusters of cells, named mammospheres, were collected by gentle centrifugation after 7 days.
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 p3.5

Data table
ID_REF VALUE
6848511 9.52611
6864895 9.94524
6766590 4.51219
6914045 4.8766
6963197 7.02739
6766588 4.51177
6995964 10.27642
6766587 5.67512
6815739 6.27532
6766586 8.24167
7012346 5.21524
6766585 7.00713
6848505 8.82057
6766584 6.24658
6848504 9.40539
6979576 5.42859
6995960 7.43643
6766583 5.45907
6963191 7.46455
6979575 6.14717

Total number of rows: 23238

Table truncated, full table size 363 Kbytes.




Supplementary file Size Download File type/resource
GSM536355.CEL.gz 24.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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