|
| Status |
Public on Jan 01, 2012 |
| Title |
Kidney_PCK_30dayold_technical rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Kidney_30 day old PCK
|
| Organism |
Rattus norvegicus |
| Characteristics |
organ: Kidney
strain: PCK
age: 30 days
|
| Treatment protocol |
All rats were fed 5LOD diet (Purina, Jefferson, WI) for the duration of the experiments.
|
| Growth protocol |
SD, FHH, PCK, FHH.Pkhd1 animals sacrificed at 30 days of age, and kidneys removed and stored in RNAleter (Ambion).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Trizol (Invitrogen, Carlsbad, CA) method according to manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
biotinylated cRNA were prepared from 100ng starting material, using Affymetrix protocol and Affymetrix 3' IVT Express Kit (GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix)
|
| |
|
| Hybridization protocol |
following fragmentation, 10ug of cRNA were hybridized for 16hr at 45oC on Affymetrix Rat Genome 230 2.0 arrays.
|
| Scan protocol |
GeneChips were washed and stained in the Affymetrix Fluidics station 450, and scanned using a 7G GeneChip Scanner 3000. Image data were quantified with Affymetrix Expression Console Software.
|
| Data processing |
The quantified raw signal intensites were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. Analysis of variation (ANOVA) was conducted using Partek Genomics Suite 6.2 (Partek Incorporated). Differentially expressed probe sets were defined as those possessing ANOVA p<0.05, and a log2 ratio >0.5 between the compared groups. Biological network analysis was performed with the Ingenuity Pathway Analysis (IPA; http://www.ingenuity.com/).
|
| |
|
| Submission date |
Oct 18, 2011 |
| Last update date |
Jan 01, 2012 |
| Contact name |
Caitlin C OMeara |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Physiology
|
| Lab |
Carol Moreno
|
| Street address |
8701 Watertown Plank Rd
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE33056 |
Expression data from polycystic kidney disease susceptible and resistant rat strains |
|
