|
| Status |
Public on Nov 10, 2006 |
| Title |
Revertant ME-B cells: breast cancer cell line |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer cell line
|
| Organism |
Mus musculus |
| Characteristics |
Small tissue segments from the 583 tumor 1 were isolated and used to establish the revertant ME-B cells. These cells show (in contrast to the ME-A cells) a downregulation of the WAP-SVT/t gene expression. These cells, that were formerly of tumor origin regain the morphology and growth characteristic of non-tumor cells. This transition occurs mostly within the first days after plating under standard tissue culture conditions (DME-medium, 10% FCS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.
|
| Label |
biotin
|
| Label protocol |
The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).
|
| |
|
| Hybridization protocol |
The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.
|
| Scan protocol |
Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.
|
| Description |
see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.
|
| Data processing |
The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.
|
| |
|
| Submission date |
Nov 08, 2006 |
| Last update date |
Nov 09, 2006 |
| Contact name |
Andreas Klein |
| E-mail(s) |
[email protected]
|
| Phone |
+49 30 450 528087
|
| Fax |
+49 30 450 52945
|
| URL |
http://www.charite.de/molbiol/bioinf/tumbiol/
|
| Organization name |
Charité (CCO)
|
| Department |
Institute of Biochemistry
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE6246 |
Gene expression profiling: breast cancer formation in WAP-SVT/t transgenic animals |
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