|
| Status |
Public on Mar 01, 2012 |
| Title |
GC_F3-Control_biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Granulosa cell from 6 months old F3 control lineage rat ovary
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell preparation date batch: 3
strain: Sprague-Dawley
gender: Female
cell: granulosa cell
developmental stage: Ovary from 6 months old rat
lineage: F3 control
|
| Treatment protocol |
Granulosa cell were isolated from 6 months old female rats of F3 generation of vinclozolin and control lineages as described earlier (Peters et al., 1999).
|
| Growth protocol |
Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003]. Subsequent F2 and F3 generations wee obtained from F1 rats.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from granulosa cells of rat ovaries after lysis 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 Granulosa cell from 6 months old ovary of F3 control lineage rat
For each mRNA microarray replica, mRNA from 4 different samples of granulosa cell originated from 4 different rats were combined - equal amount of mRNA from each.
|
| 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. Granulosa cell preparation date batch effect was removed.
|
| |
|
| Submission date |
Nov 02, 2011 |
| Last update date |
Mar 01, 2012 |
| 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 (2) |
| GSE33423 |
Environmental Toxicants Induce Epigenetic Transgenerational Inheritance of Ovarian Disease [Affymetrix] |
| GSE59278 |
Environmentally induced epigenetic transgenerational inheritance of ovarian disease |
|
