|
| Status |
Public on Oct 01, 2009 |
| Title |
Non estrogen treated endometrium at day 13, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Non estrogen treated endometrium at day 13, collected on day 13 of psuedo pregnancy
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Endometrium
age: 8-10 months
genotype: cross bred cyclic gilts
time of pseudo-pregnancy: 13 days
|
| Treatment protocol |
Endometrium was collected on either days 13 or 15 of pseudo pregnancy following a flushing of the uteri with 20 mL of physiological saline. Endometrium was placed into a wirl pouch, snap-frozen in liquid nitrogen and then placed in the -80C until utilized.
|
| Growth protocol |
Gilts were group housed. Estrus detection was conducted twice daily. Gilts were treated with estrogen or corn oil at the onset of their second estrus following a normal estrous cycle, and again 24 hours later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
cRNA were prepared by the GeneChip One-Cycle target labeling kit according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression from endometrium
|
| Data processing |
[1] dChip’s method of invariant set normalization in which the chip with the median intensity value was used as the baseline against which the brightnesses of the remaining chips were adjusted in order to be of a comparable level. [2] Standardization was conducted by calculating model-based expression indices (MBEI) using dChip’s Perfect-Match (PM)-only model. This additional modeling reduces the variance of expression level estimates by accounting for probe differences. [3] Data were log transformed to improve statistical performance by approximating a normal distribution within each gene. The log base2 scale is favorable because each unit difference represents a 2-fold difference.
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| |
|
| Submission date |
Sep 30, 2009 |
| Last update date |
Sep 30, 2009 |
| Contact name |
morgan dean ashworth |
| E-mail(s) |
morgan.ashworth@yale.edu
|
| Phone |
5803368467
|
| Organization name |
yale school of medicine
|
| Department |
OB/GYN reproductive immunology
|
| Lab |
Lab 309C
|
| Street address |
333 cedar street
|
| City |
new haven |
| State/province |
CT |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE18343 |
Expression data from estrogen disrupted endometrium |
|
