|
| Status |
Public on Jun 13, 2010 |
| Title |
P4_Ovary_Control_biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
P4 Ovary incubated for 48 hours with no treatment
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
gender: Female
tissue: ovary
developmental stage: day P4 incubated for 2 more days
|
| Treatment protocol |
For each ovary sample from which RNA was collected for microarrays, 2-3 ovaries per well were cultured with media changes every 24 hours for two days in the absence (controls) or presence (treated) CTGF (human connective tissue growth factor)(50ng/mL, PeproTech Inc., NJ USA). Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together.
|
| Growth protocol |
Four-day old female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously [Dole, G., et al., 2008].
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, ssDNA were hybridized on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 4500.
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.
|
| Description |
Gene expression data from rat P4 Ovary incubated for 48 hours with no treatment
|
| Data processing |
The data were analyzed with Partek Genomic Suite 6.5 beta software (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.
|
| |
|
| Submission date |
Feb 13, 2010 |
| Last update date |
Feb 16, 2010 |
| Contact name |
Michael K Skinner |
| E-mail(s) |
skinner@mail.wsu.edu
|
| Organization name |
WSU
|
| Department |
SBS
|
| Street address |
Abelson 507
|
| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99163 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE20324 |
Gene Bionetwork Analysis of Ovarian Primordial Follicle Development |
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