|
| Status |
Public on Sep 10, 2008 |
| Title |
Conceptus Morphology_Tubular (20-80mm)_Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Tubular embryos
|
| Organism |
Sus scrofa |
| Characteristics |
Crossbred, cyclic gilts were approximately 8-10 months of age. Tubular (20-80 mm) embryos were collected on approximately day 11-12 of gestation.
|
| Treatment protocol |
Conceptuses were collected by flushing the uteri with 20 mL of physiological saline. Morphological data of the embryos were recorded and the conceptuses were placed into a cryogenic vial, 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 mated naturally with an intact boar at the onset of their second estrus following a normal estrous cycle and again 24 hours later.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We utilized RNAwiz (Ambion). According to the manufacturers recommendations.
|
| Label |
GeneChip DNA Labeling Reagent
|
| 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 |
Tubular embryos (20-80 mm) collected on day 11-12 of gestation.
|
| Data processing |
1st. 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. 2nd. 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. 3rd. 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.
|
| |
|
| Submission date |
Sep 08, 2008 |
| Last update date |
Sep 09, 2008 |
| Contact name |
Jason W Ross |
| E-mail(s) |
jwross@iastate.edu
|
| Organization name |
Iowa State University
|
| Department |
Animal Science
|
| Street address |
2356E Kildee Hall
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL3533 |
| Series (1) |
| GSE12705 |
Differential gene expression during porcine conceptus trophoblastic elongation and attachment to the uterine epithelium |
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