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E-GEOD-6208 - Transcription profiling of rat kidney from dahl salt-sensitive (S) and the renal protective S.SHR(2) congenic strain

Submitted on 1 November 2006, released on 14 June 2008, last updated on 10 June 2011
Rattus norvegicus
Samples (18)
Array (1)
Protocols (4)
The study sought to investigate differences in onset and progression of renal disease in the Dahl salt-sensitive (S), S.SHR(2) congenic, and spontaneously hypertensive rat (SHR) using a time-course. The data clearly demonstrates that the locus on chromosome 2 has a major and sustained ability to attenuate renal damage. As early as week 4, significant interstitial changes were observed between the S and the congenic which preceded any significant difference in proteinuria. Gene expression profiling was performed at week 4, 12, and 20 using kidney from the S and S.SHR(2) congenic to: (1) identify expression differences of positional candidates within the QTL region; (2) correlate temporal gene expression changes between the S and congenic with degree of renal damage; and (3) identify biochemical pathways potentially involved in the attenuated renal damaged observed in the congenic. Gene pathway analysis (Ingenuity® Systems) performed at week 4, 12, and 20 revealed that pathways involved in cellular assembly and organization, cellular movement, and immune response were controlled differently between the S and congenic. Considering all the data, the chromosome 2 congenic appears to attenuate renal damage primarily through an altered fibrotic response. Experiment Overall Design: DNA microarray analysis was performed using Affymetrix Genechip® Rat Genome 230 2.0 array at three timepoints. The chip contains 31,000 probe sets from more than 30,000 transcripts on one array. Three male S and three male S.SHR(2) congenic were selected at random from each group test for proteinruia at week 4, 12 and 20. Kidney was cut into ~ 0.5cM size cubes, suspended in RNAlater (Ambion, Austin, TX) and stored overnight at 4ºC. RNA was extracted using Trizol® reagent (Invitrogen, Carlsbad, CA) and purified using Mini RNeasy kit (Qiagen,Valencia, CA ) according to manufacturer’s protocols. RNA quality was assessed by an OD260/280 ratio > 2.0 and visually by ethidium bromide staining on an agarose gel. Experiment Overall Design: Biotinylated cRNA was synthesized from 10 ug of total RNA using the One-Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA) as directed by the user manual. cRNA quality for each sample was assessed by hybridization of 5ug adjusted kidney cRNA to Affymetrix Genechip® Test3 array. Subsequently, 15ug adjusted kidney cRNA was hybridized to the Genechip® Rat 230 2.0 array. Hybridized chips were automatically washed, stained and scanned at the Medical University of Ohio Bioinformatics & Proteomics/Genomics Program gene array facility using Affymetrix equipment.
Experiment types
transcription profiling by array, unknown experiment type
Investigation descriptionE-GEOD-6208.idf.txt
Sample and data relationshipE-GEOD-6208.sdrf.txt
Raw data (1)
Processed data (1)
Array designA-AFFY-43.adf.txt
R ExpressionSetE-GEOD-6208.eSet.r