Comparison of renal transcript levels in Dahl Salt-sensitive (S) rat with S.R congenic rat containing a BP QTL
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE1775 | GEO | 2004/09/20
SECONDARY ACCESSION(S): PRJNA90325
REPOSITORIES: GEO
Similar Datasets
Project description:Kidney samples from three Dahl Salt-sensitive S rats were compared with kidney samples from three S.R(9)x3A congenic rats.
2007-09-13 | E-GEOD-1775 | biostudies-arrayexpress
Project description:Gene expression profiling of kidney tissue from 5 week old Dahl salt sensitive rats and congenic strain of Chr.10 Dahl salt sensitive rats. Keywords: other
2003-08-20 | GSE413 | GEO
Project description:The overlap of congenic regions in an earlier substitution mapping study suggested the location of two blood pressure quantitative trait loci (QTL)-containing regions in the q-terminus of rat chromosome 3, QTL1 and the more distal, QTL2. Male SS/jr rats and two congenic substrain rats S.R(D3Mco36-D3Mco46) and S.R(D3Mco36-D3Got166) were maintained on a low salt (0.4% NaCl Harlan Teklad diet TD7034) diet until 39-41 days of age. These 3 rat strains will be hereafter referred to as S, S.R(ET3x1), and S.R(ET3x2), respectively. At 39-41 days of age, half of the rats from each strain were fed a high (4% NaCl Harlan Teklad diet TD83033) salt diet and water ad libitum for 24 hours. Both congenic substrains carry SR/jr (R)-rat alleles for QTL2 on an S-rat genetic background, while S.R(ET3x2) also carries R-rat alleles for QTL1. Renal gene expression analysis was used to identify differentially expressed genes or genes with altered activity within the S.R(ET3x2) congenic region. Keywords: strain differences in response to dietary changes
2015-08-28 | GSE12424 | GEO
Project description:The overlap of congenic regions in an earlier substitution mapping study suggested the location of two blood pressure quantitative trait loci (QTL)-containing regions in the q-terminus of rat chromosome 3, QTL1 and the more distal, QTL2. Male SS/jr rats and two congenic substrain rats S.R(D3Mco36-D3Mco46) and S.R(D3Mco36-D3Got166) 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. These 3 rat strains will be hereafter referred to as S, S.R(ET3x1), and S.R(ET3x2), respectively. Both congenic substrains carry SR/jr (R)-rat alleles for QTL2 on an S-rat genetic background, while S.R(ET3x2) also carries R-rat alleles for QTL1. Renal gene expression analysis was used to identify differentially expressed genes or genes with altered activity within the S.R(ET3x2) congenic region. Keywords: strain differences in response to dietary changes
2015-08-28 | GSE12423 | GEO
Project description:Gene expression profiling of kidney tissue from 5 week old Dahl salt sensitive rats and congenic strain of Chr.10 Dahl salt sensitive rats.
2008-04-03 | E-GEOD-413 | biostudies-arrayexpress
Project description:Evidence from multiple linkage and genome-wide association studies suggest that human chromosome 2 (HSA2) contains alleles that influence blood pressure (BP). Homologous to a large segment of HSA2 is rat chromosome 9 (RNO9), to which a BP quantitative trait locus (QTL) was previously mapped. The objective of the current study was to further resolve this BP QTL. Eleven congenic strains with introgressed segments spanning <81.8kb to <1.33Mb were developed by introgressing genomic segments of RNO9 from the Dahl salt-resistant (R) rat onto the genome of the Dahl salt-sensitive (S) rat and tested for BP. The congenic strain with the shortest introgressed segment spanning <81.8kb significantly lowered BP of the hypertensive S rat by 25 mm Hg and significantly increased its mean survival by 45 days. In contrast, two other congenic strains had increased BP compared with the S. We focused on the <81.8kb congenic strain which represents the shortest genomic segment to which a BP QTL has been definitively mapped to date in any species. Sequencing of this entire region in both S and R rats detected 563 variants. The region did not contain any known or predicted rat protein coding genes. Further, a whole genome renal transcriptome analysis between S and the <81.8kb S.R congenic strain revealed alterations in several critical genes implicated in renal homeostasis. Taken together, our results provide the basis for future studies to examine the relationship between the candidate variants within the QTL region and the renal differentially expressed genes as potential causal mechanisms for BP regulation. Six male S control and 6 male congenic S.R(9)x3x2Bx1x8 rats born on the same day were selected, weaned at 30 days of age, and caged with 1 congenic and 1 S rat per cage. They were raised on a High-salt (2%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley) and sacrificed at 53 days of age and total RNAs were isolated from the kidney. The isolated RNA from two animals were pooled together and considered as one biological sample. Three such RNA samples from S and congenic rats were used for the cRNA preparation. cRNA was prepared and fragmented as suggested by Affymetrix technical manual, and simultaneously hybridized (15 µg adjusted cRNA for each chip) to Rat Expression Array 230 2.0 (3' IVT Expression Analysis). Statistical analyses of the microarray data were performed using R statistical package (version 2.8.1).
2010-07-15 | E-GEOD-22515 | biostudies-arrayexpress
Project description:We used Affymetrix GeneChips to expression profile kidneys from Dahl salt-senstive hypertensive inbred strain and less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain to identify genes downstream of Adamts16 (the function of Adamts16 has yet to be fully delineated). The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. It is hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. We further hypothesize that gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S result from sequence differences between the S and LEWIS alleles of Adamts16. Lastly, the downstream genes differentially regulated by the Adamts16 alleles may provide insight pertaining to the mechanism of blood pressure differences. Gene expression differences resulting from these kidney comparisons will be compared to the gene expression profiling experiments comparing siRNA-mediated knockdown of Adamts16 in NRK-52E kidney cells versus scrambled siRNA control. Experiment Overall Design: Kidney RNA from 3 Dahl salt-sensitive rats was extracted for target preparation and hybridization onto Affymetrix GeneChips. We also isolated kidney RNA from 3 S.LEW(D1MCO4x1x3Bx1) congenic rats for target preparation and hybridization onto Affymetrix GeneChips.
2008-11-13 | E-GEOD-12725 | biostudies-arrayexpress
Project description: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. Keywords: time course
2007-11-01 | GSE6208 | GEO
Project description:Evidence from multiple linkage and genome-wide association studies suggest that human chromosome 2 (HSA2) contains alleles that influence blood pressure (BP). Homologous to a large segment of HSA2 is rat chromosome 9 (RNO9), to which a BP quantitative trait locus (QTL) was previously mapped. The objective of the current study was to further resolve this BP QTL. Eleven congenic strains with introgressed segments spanning <81.8kb to <1.33Mb were developed by introgressing genomic segments of RNO9 from the Dahl salt-resistant (R) rat onto the genome of the Dahl salt-sensitive (S) rat and tested for BP. The congenic strain with the shortest introgressed segment spanning <81.8kb significantly lowered BP of the hypertensive S rat by 25 mm Hg and significantly increased its mean survival by 45 days. In contrast, two other congenic strains had increased BP compared with the S. We focused on the <81.8kb congenic strain which represents the shortest genomic segment to which a BP QTL has been definitively mapped to date in any species. Sequencing of this entire region in both S and R rats detected 563 variants. The region did not contain any known or predicted rat protein coding genes. Further, a whole genome renal transcriptome analysis between S and the <81.8kb S.R congenic strain revealed alterations in several critical genes implicated in renal homeostasis. Taken together, our results provide the basis for future studies to examine the relationship between the candidate variants within the QTL region and the renal differentially expressed genes as potential causal mechanisms for BP regulation.
2010-07-15 | GSE22515 | GEO
Project description:To get more insight in cause and consequences of proteinuria, we studied glomerular gene expression patterns before and after the onset of increased urinary albumin excretion in a proteinuric rat strain. Spontaneously proteinuric Dahl salt-sensitive rats (Dahl SS) were compared to non-proteinuric, spontaneously hypertensive rats (SHR). In Dahl SS, UAE significantly increased starting from week 5 of age. Glomerular RNA profiles of 4- and 6 week-old rats were studied by Affymetrix microarrays. Keywords: Time course analysis
2009-01-01 | GSE13810 | GEO