|
| Status |
Public on Jun 22, 2020 |
| Title |
Mammary gland tumor Rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
Mammary gland tumor Rep 2
|
| Organism |
Mus musculus |
| Characteristics |
gender: Female
strain: C57Bl/6
|
| Treatment protocol |
Normal mammary gland was recovered from female mices that were not exposed to either MPA nor DMBA. Hyperplastic mammary glands were recovered from female mice that underwent MPA/DMBA protocol but did not develop any tumor. Mammary gland tumors were recovered from female mice once the tumor reach the size of 0.7-1 cm^2
|
| Growth protocol |
Fifty mg slow-release (90 days) medroxyprogesterone acetate (MPA) pellets (Innovative Research of America) were implanted subcutaneously by surgery into 6-9 week-old female (day 0). Mice were administered 200 µL of a 5 mg mL-1 7,12-dimethylbenz[a]anthracene (DMBA; from Sigma-Aldrich) solution in corn oil (Sigma-Aldrich), by oral gavage once a week on weeks 1, 2, 3, 5, 6 and 7 after implantation of the MPA pellet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary gland tissue was removed from the mice and RNA freshly extracted using Qiagen RNeasy kits.
|
| Label |
biotin
|
| Label protocol |
200 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Affymetrix) . Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.
|
| |
|
| Hybridization protocol |
After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MTA1.0 (Affymetrix) at 45°C for 17 hours
|
| Scan protocol |
After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G
|
| Data processing |
The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. RMA normalization is performed using Partek software with Affymetrix CDF file.
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| |
|
| Submission date |
May 26, 2020 |
| Last update date |
Jun 26, 2020 |
| Contact name |
Aitziber Buque Martinez |
| Organization name |
Weill Cornell Medical College
|
| Department |
Radiation Oncology
|
| Street address |
1300 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL20258 |
| Series (1) |
| GSE151197 |
M/D-tumors vs non´-tumor mammary gland tissues |
|
