|
| Status |
Public on Aug 28, 2015 |
| Title |
ET3x2_rat_kidney_RNA_pool_K_RAE230B |
| Sample type |
RNA |
| |
|
| Source name |
ET3x2 rat left kidney
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: S.R(ET3x2), age: 67-69 days, gender: male, tissue: left kidney
|
| Treatment protocol |
Male SS/jr (S) rats, S.R(ET3x1) substrain rats and S.R(ET3x2) substrain rats were maintained on a low salt (0.4% NaCl Harlan Teklad diet TD7034) diet until 39-41 days of age and then fed an intermediate (2% NaCl Harlan Teklad diet TD94217) salt diet for 28 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The left kidneys from each rat were homogenized separately in a guanidine thiocyanate/phenol solution (Ultraspec, Biotecx Laboratories, Houston, TX), extracted with chloroform and isolated using RNA Tack Resin (Biotecx Laboratories). Total RNA was further purified by ethanol precipitation and absorption to a column (RNeasy, Qiagen, Valencia, CA) facording to the manufacturer's instructions. RNA integrity was assessed by 1) electrophoretic size-fractionation on 1% agarose gels under denaturing conditions and 2) hybridization of newly made cRNA probes to TestChips (Affymetrix). Double-stranded cDNA was synthesized (separately) from 15 μg total RNA from each pool of kidney RNA (four pools/strain) using reverse transcriptase (SuperScript II, InVitrogen, Carlsbad, CA) and T7-(dT)24 as the oligonucleotide primer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was synthesized using a kit (Enzo Bioarray High Yield RNA transcript Labeling Kit, Enzo Diagnostics, Farmingdale, NY) and cRNAs were purified on columns (RNeasy mini kit, Qiagen).
|
| |
|
| Hybridization protocol |
Each cRNA was fragmented according to the protocol in the Affymetrix GeneChip Expression Analysis manual with quality assessed by hybridization of a 5 μg aliquot to a test chip (TestChip3, Affymetrix). Fragmented cRNA probe (5 μg) was then hybridized to each of a set of 2 rat GeneChips (RAE230B and RAE230B; Affymetrix). Hybridization, washing, and staining with streptavidin-phycoerythrin was performed at the University of Toledo Health Science Campus Genomics Core Facility according to the manufacturer's (Affymetrix) instructions.
|
| Scan protocol |
Scanning was performed at the University of Toledo Health Science Campus Genomics Core Facility according to the manufacturer's (Affymetrix) instructions.
|
| Description |
Gene expression data from S.R(ET3x2) congenic rat left kidney RNA pool K (rats 39830, 39831 and 39822)
|
| Data processing |
Probe set expression measures were calculated from probe-level data using RMAExpress v0.5 software with background adjustment, quantile normalization and log 2 transformation
|
| |
|
| Submission date |
Aug 14, 2008 |
| Last update date |
Aug 28, 2015 |
| Contact name |
Andrew John McSweeny |
| E-mail(s) |
andrew.mcsweeny@utoledo.edu
|
| Phone |
+1 419 383 4182
|
| Fax |
+1 419 383 2871
|
| URL |
http://hsc.utoledo.edu/grad/cvmd/faculty.html
|
| Organization name |
University of Toledo College of Medicine
|
| Department |
Physiology & Pharmacology: CVMD Track
|
| Lab |
George T. Cicila
|
| Street address |
3000 Arlington Avenue Room # 209, Mail Stop #1008
|
| City |
Toledo |
| State/province |
OH |
| ZIP/Postal code |
43614 |
| Country |
USA |
| |
|
| Platform ID |
GPL342 |
| Series (2) |
| GSE12423 |
Renal Expression of Dahl SS/Jr (S) and Congenic Rats after 28 days of dietary salt elevation |
| GSE29078 |
Dietary Salt effects on Renal Expression of Dahl SS/Jr (S) and Congenic Rats |
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