|
| Status |
Public on Sep 15, 2011 |
| Title |
C1_rat_mammary gland |
| Sample type |
RNA |
| |
|
| Source name |
control group
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Lewis rats
gender: Female
age: 3 month old
physiological stage: Met-estrus
tissue type: Mammary gland Inguinal left
|
| Treatment protocol |
Rats were randomly assigned to three groups (5 rats per group): control (C), pregnancy (P) and hormone treatment (H). The P group animals had a full-term pregnancy (21-23 days) and rats in the group H were implanted subcutaneously on the dorsal midline with two silastic capsules [(0.078 inch inner diameter, 0.125 inch outer diameter) x 2 cm long; Dow Corning, Midland, MI) filled separately with 100 μg ethynyl estradiol (Sigma, St. Louis, MO) packed in a cellulose matrix (Sigma) and 30 mg of megesterol acetate (Sigma) for 21 days. The control animals had neither the hormone treatment nor being pregnant. The animals in C and P groups were also implanted with sham capsules filled with cellulose matrix only.
|
| Growth protocol |
Fifteen, 3 month old post-pubertal virgin Lewis rats were kept in the University of Vermont small animal care facility. Rats were housed in the air and temperature-controlled cage shelves on a 12-hour light/dark cycle and were fed rat chow (RMH 3000, Lab Diet, Scott Distributing, Inc. MA) and water ad libitum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared using the reagents of NuGEN Ovation V2 from 80 ng of total RNA
|
| |
|
| Hybridization protocol |
Fragmentation and Biotin labeling was performed using 4ug of cDNA using the NuGEN Encore reagents and h ybridized to the Rat 230 2.0 GeneChip for 16 hr at 45C at 60 rpm, double stained with streptavidin-PE using the Affymetrix 450 fluidics station and scanned with the Affymetrix 3000-G7 scanner
|
| Scan protocol |
The gene chips were scanned with Affymetrix 3000-G7 scanner
|
| Description |
Gene expression data from Rat inguinal mammary gland during the metestrus phase of the reproductive cycle
|
| Data processing |
Raw oligonucleotide array data image is summarized by one probe intensity using Affymetrix GCOS software. Probe statistics are background corrected, normalized, and summarized using the R (R Development Core Team, 2009)/Bioconductor (Gentleman et al., 2004) aroma affymetrix package (Bengtsson et al., 2008), which implements the Robust Multichip Average (RMA) statistic of Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003). Affymetix MAS5 presence/absence calls were made using the Bioconductor affy package (Gautier et al., 2004) and provided as a Series Supplementary files [analysis_results.txt]
|
| |
|
| Submission date |
Sep 14, 2011 |
| Last update date |
Sep 15, 2011 |
| Contact name |
Yogi Misra |
| E-mail(s) |
[email protected]
|
| Phone |
8023998334
|
| Organization name |
UVM
|
| Department |
Animal Science
|
| Lab |
Zhao
|
| Street address |
570 Main street
|
| City |
Burlington |
| State/province |
Vermont |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE32125 |
Mammary Gland Morphological and Gene Expression Changes Underlying Pregnancy Protection of Breast Cancer Tumorigenesis |
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