|
| Status |
Public on Mar 06, 2015 |
| Title |
Shp2 knockout mammospheres, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
mammospheres, Shp2 knockout
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: FVB/N
genotype/variation: MMTV-PyMT;Shp2fl/fl
cell type: primary mammary tumor cells
treatment: CreERT2 retrovirus infection
|
| Treatment protocol |
Mammospheres were treated with 50 nM 4-OHT for 2 hours and collected for RNA isolation 5 days later.
|
| Growth protocol |
Primary mammary tumor cells were cultured as mammospheres under the serum-free, non-attached conditions containing EGF, FGF and B27.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA and subsequent purification by QIAGEN RNeasy Kits was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
The chips were scanned on an Affymetrix GeneChip Scanner.
|
| Description |
LLX--06-CreERT2-430A-2
Mammary tumor cells are derived from mammary tumors of MMTV-PyMT mice, a model for breast cancer.
Mammary tumor cells cultured as mammospheres for 12 days.
Mammospheres infected with CreERT2 retrovirus.
|
| Data processing |
Array data were analyzed using Expression Console and were normalized with MAS5.0. Normalized data were used for calculating fold changes of deregulated genes using Student's test. Only genes with a false discovery rate (FDR) adjusted p-value <0.05 and at least 1.5 fold differential expression were included in the analysis.
|
| |
|
| Submission date |
Sep 03, 2013 |
| Last update date |
Mar 06, 2015 |
| Contact name |
Linxiang Lan |
| Organization name |
Max-Delbrueck-Center for Molecular Medicine
|
| Department |
Cancer Research Program
|
| Street address |
Robert-Roessle-Str. 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL8321 |
| Series (2) |
| GSE50516 |
Shp2 Signaling Suppresses Senescence in PyMT-induced Mammary Gland Cancer in Mice [Mouse430A_2 array] |
| GSE50518 |
Shp2 Signaling Suppresses Senescence in PyMT-induced Mammary Gland Cancer in Mice |
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