|
| Status |
Public on Jul 16, 2013 |
| Title |
Mouse mammary gland Ccnd1-/- E2 Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
mammary gland_Ccnd1-/-_E2
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Ccnd1-/-
treated with: estradiol releasing pellets
tissue: mouse mammary gland
|
| Treatment protocol |
Virgin Ccnd1-/- and Ccnd1+/+ mice were overiectomized and allowed to recover for 2 after the surgery. Mice from each genotype split into 2 groups and treated with placebo control or estradiol releasing pelles (0.72mg, 60 day release). Mice were treated for 7 days and then sacrifised.
|
| Growth protocol |
No specific growth protocol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol reagent (Invitrogen) as per manufacturers' guidelines.
|
| Label |
Biotin
|
| Label protocol |
The double stranded cDNA was used as a template to generate biotinylated cRNA using Bioarray HighYield RNA Transcription Labeling Kit (Enzo) and the labeled cRNA purified by GeneChip Sample Cleanup Module (Affymetrix)
|
| |
|
| Hybridization protocol |
15µg of cRNA was fractionated to produce fragments between 35–200 bp using 5x Fragmentation buffer provided in the Cleanup Module, followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).
|
| Scan protocol |
Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.
|
| Data processing |
The data were analyzed and normalized by Robust Multi-array Average (RMA) algorithm using affylmGUI (1.14.0) running limma version 2.9.16 within the language and environment program R (2.4.1).
|
| |
|
| Submission date |
Jul 15, 2013 |
| Last update date |
Jul 16, 2013 |
| Contact name |
Mathew Casimiro Casimiro |
| Organization name |
Thomas Jefferson University
|
| Department |
233 South 10th St, Rm 1035
|
| Lab |
Philadelphia
|
| Street address |
233 South 10th St, Rm 1035
|
| City |
19107 |
| State/province |
United States |
| ZIP/Postal code |
Mathew Casimiro |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE48884 |
Cyclin D1 determines estrogen depependent signaling in mouse mammary gland. |
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