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Sample GSM312736 Query DataSets for GSM312736
Status Public on Aug 28, 2015
Title S_rat_high_salt_diet_S7417_kidney_RNA_RAE230B
Sample type RNA
 
Source name S rat S7417 left kidney
Organism Rattus norvegicus
Characteristics strain: SS/jr, diet: high salt (Harlan Teklad TD83033, 4% NaCl), age: 40-42 days, gender: male, tissue: left kidney
Treatment protocol Age-matched male S (n=10), S.R(ET3x1) (n=8), and S.R(ET3x2) (n=8) rats were bred, housed, and studied concomitantly to minimize envi¬ronmental effects. Rats were weaned at 30 days of age onto a low salt diet (0.4% NaCl, Harlan Teklad diet TD7034) and water ad libitum. At 39-41 days of age one-half of rats from each strain group were switched to a 4% NaCl diet (Harlan Teklad diet TD83033) and water ad libitum for 24 hours. All rats were then killed by pentobarbital overdose. Kidneys were removed, decapsulated, blotted dry, and weighed. The kidneys of each rat were then processed separately for isolation of total RNA.
Extracted molecule total RNA
Extraction protocol A single rat kidney RNA sample was used for each of 26 RAE230A/B chipsets [10 S-rat samples, 8 S.R(ET3x1) samples, and 8 S.R(ET3x2) samples]. Total RNA was isolated from the kidneys of each rat separately, essentially as described (Lee et al 2003). Briefly, kidneys were homogenized 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) following the manufacturer's instructions. Kidney 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).
Label biotin
Label protocol Oligonucleotide microarray analysis was performed essentially as described in Lee et al. (2005) using the Affymetrix Rat Genome RAE230 array set (GeneChips 230A and 230B) according to the manufacturer’s protocol. Double-stranded cDNA was synthesized from 15 microgram total RNA from each rat kidney RNA preparation using reverse transcriptase (SuperScript II, InVitrogen, Carlsbad, CA) and T7-(dT)24 as the oligonucleotide primer. 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 g aliquot to a test chip (TestChip3, Affymetrix). Fragmented cRNA probe (5 g) was then hybridized to each of a set of 2 rat GeneChips (RAE230A and RAE230B; Affymetrix).
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 SS/jr rat S7417 left kidney after 24 hours on high salt diet
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)
GSE12424 Renal Expression of Dahl SS/Jr (S) and Congenic Rats after 24 hours of Dietary Salt Loading
GSE29078 Dietary Salt effects on Renal Expression of Dahl SS/Jr (S) and Congenic Rats

Data table header descriptions
ID_REF
VALUE RMA, background adjusted, quantile normalized, log 2 transformed

Data table
ID_REF VALUE
1367452_at 10.751097
1367453_at 10.322083
1367454_at 9.977838
1367455_at 11.212576
1367456_at 11.482091
1367457_at 9.64569
1367458_at 8.902886
1367459_at 12.170644
1367460_at 11.64441
1367461_at 9.225711
1367462_at 10.716764
1367463_at 10.975457
1367464_at 8.828724
1367465_at 10.255052
1367466_at 10.666362
1367467_at 11.35441
1367468_at 9.177085
1367469_at 11.175462
1367470_at 11.120739
1367471_at 9.406221

Total number of rows: 15333

Table truncated, full table size 299 Kbytes.




Supplementary file Size Download File type/resource
GSM312736.CEL.gz 2.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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