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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of SBH/y rats vs SBN/y rats under basal conditions and after salt loading

ABSTRACT: Gene expression was studied in whole kidneys in a 2 x 2 design. SBH/y were contrasted with SBN/y under basal conditions and after salt loading. Thus, four groups were studied altogether. Five rats were used in each group. Altogether, 20 animals were used, and each animal was studied separately. Gene expression was done in kidney. Differential gene expression was measured 4 weeks after initiation of salt loading. At that time point hypertension invariably evolves fully in SBH/y but not in SBN/y.

Affymetrix CHP files are available on request from arrayexpress@ebi.ac.uk

ORGANISM(S): Rattus norvegicus

SUBMITTER: Oliver Hummel

PROVIDER: E-MEXP-157 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of hypertension-related genes through an integrated genomic-transcriptomic approach.

Yagil Chana C Hubner Norbert N Monti Jan J Schulz Herbert H Sapojnikov Marina M Luft Friedrich C FC Ganten Detlev D Yagil Yoram Y

Circulation research 20050224 6

In search for the genetic basis of hypertension, we applied an integrated genomic-transcriptomic approach to identify genes involved in the pathogenesis of hypertension in the Sabra rat model of salt-susceptibility. In the genomic arm of the project, we previously detected in male rats two salt-susceptibility QTLs on chromosome 1, SS1a (D1Mgh2-D1Mit11; span 43.1 cM) and SS1b (D1Mit11-D1Mit4; span 18 cM). In the transcriptomic arm, we studied differential gene expression in kidneys of SBH/y and S ...[more]

PMID: 15731461

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Expression data from male rat kidney: pathophysiology of proteinuria

Project description:This study was designed to investigate gene expression in kidneys of adult Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria. Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria The experiment was performed in male animals after weaning. Four groups were studied: SBN/y with 2 kidneys (ham uni-nephrectomy), SBN/y after uni-nephrectomy, SBH/y with 2 kidneys (sham uninephrectomy) and SBH/y after uni-nephrectomy. Animals were provided rat chow ad libitum. At age 4 months, 3 months after uninephrectomy or sham operation, animals were sacrificed under ether anesthesia, killed by exsanguination and the kidneys were rapidly removed and snap frozen with liquid nitrogen. The kidneys were stored at -800C until RNA was extracted for the differentiale xpression experiment.

2009-02-03 | E-GEOD-14676 | biostudies-arrayexpress

Expression data from female rat kidney: pathophysiology of proteinuria

Project description:This study was designed to investigate gene expression in kidneys of adult female Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria. Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria The experiment was performed in female animals after weaning. Four groups were studied: SBN/y with 2 kidneys (sham uni-nephrectomy), SBN/y after uni-nephrectomy, SBH/y with 2 kidneys (sham uninephrectomy) and SBH/y after uni-nephrectomy. Animals were provided rat chow ad libitum. At age 5 months, 4 months after uninephrectomy or sham operation, animals were sacrificed under ether anesthesia, killed by exsanguination and the kidneys were rapidly removed and snap frozen with liquid nitrogen. The kidneys were stored at -800C until RNA was extracted for the differential expression experiment.

2009-01-31 | E-GEOD-14666 | biostudies-arrayexpress

Metaproteomics of the Resistant Starch-fed Chronic Kidney Disease Rats

Project description:Background- Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by metaproteomics, gaining new insight into the host-microbiome interaction. Methods- Differences between cecum contents in CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins. Results - 5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information derived from metaproteomics data surpassed previous 16S RNA analysis, and reached species resolutions for moderately abundant taxonomic groups. In particular, the Ruminococcaceae family becomes well resolved – with butyrate producers and amylolytic species such as R. bromii clearly visible and significantly higher while fibrolytic species such as R. flavefaciens are significantly lower with resistant starch feeding. The observed changes in protein patterns are consistent with fiber-associated improvement in CKD phenotype. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Conclusions- Metaproteomics analysis of cecum contents of CKD rats with and without resistant starch supplementation reveals changes within gut microbiota at unprecedented resolution, providing both functional and taxonomic information. Proteins and organisms differentially abundant with RS supplementation point toward a shift from mucin degraders to butyrate producers.

2018-12-18 | PXD008845 | Pride

Transcription profiling of liver response to hypoxia treatment of parental salt sensitive (SS) and consomic Brown Norway (SS6BN) rat strain SS6BN rats are derived from introgression of chromosome 6 from BN rats into the SS genetic background

Project description:Examination of gene expression associated with hypoxia treatment of parental salt sensitive (SS) and consomic Brown Norway (SS6BN) rat strain. SS6BN rats are derived from introgression of chromosome 6 from BN rats into the SS genetic background.

2005-01-01 | E-TIGR-70 | biostudies-arrayexpress

Transcription profiling of rat kidney response to hypoxia treatment of parental salt sensitive (SS) and consomic Brown Norway (SS6BN) rat strain SS6BN rats are derived from introgression of chromosome 6 from BN rats into the SS genetic background

2005-01-01 | E-TIGR-69 | biostudies-arrayexpress

Red-fleshed apples rich in anthocyanins and white-fleshed apples poor in anthocyanins modulate aorta and heart proteome in hypercholesterolemic rats. The AppleCOR study

Project description:New mechanisms-of-action of anthocyanins (ACNs) provided by a red-fleshed apple compared with a white-fleshed apple ACN-poor, and with an ACN-rich extract on the proteome profile of aorta and heart as cardiovascular key tissues were determined. Hypercholesterolemic Wistar rats were separated into the corresponding groups to analyze the proteomic profile of the aorta and heart tissues using nano-liquid chromatography coupled to mass-spectrometry. Red-fleshed apple downregulated CRP, C1QB and CFP related-inflammation. White-fleshed apple reduced C1QB, CFB, CFD, C3, and C9 related to the complement system, reduced MB and CP related to iron metabolism, and increased ME1, PKM, and PC related to energy homeostasis. ACN-rich extract increased FMOD, TAGLN, and CAP1 related to cellular structure and decreased PRKACA, IQGAP1, and HSP90AB1 related to cellular signaling. Red-fleshed apple rich in ACNs suggested an anti-inflammatory effect while white-fleshed apple reduced the complement system protein-related. An apple matrix effect reduced inflammatory proteins regardless their ACN content.

2022-04-04 | PXD018885 | Pride

Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging

Project description:Using RNA-seq, 39 cerebral cortex RNA samples were sequenced. The study design was as follows: Ad libitum fed rats at 6 months (n=3, 6 individuals pooled), 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Calorie restricted rats at 6 months (n=3, 6 individuals pooled), 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Rats fed alpha lipoic acid as a supplement to ad libitum at 12 months (n=3, 6 individuals pooled) and 28 months (n=3, 6 individuals pooled). Diet switching groups, where diet was changes at 12 months; 28 month ad libitum switched to calorie restriction (n=3, 6 individuals pooled), 28 month calorie restriction switched to ad libitum (n=3, 6 individuals pooled), 28 month ad libitum plus lipoic acid switched to calorie restriction (n=3, 6 individuals pooled), 28 month calorie restriction switched to ad libitum plus lipoic acid (n=3, 6 individuals pooled). Transcriptional profiling of the ageing cerebral cortex at 6, 12 and 28 months and the effect of diet on age and longevity, using carlorie restriction and alpha lipoic acid supplementation

2015-11-22 | E-GEOD-57110 | biostudies-arrayexpress

Gene expression profiles in heterogeneous stock rats that differ in glucose tolerance

Project description:Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits. We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance HS rats were euthanized at 17 weeks of age and liver was immediately frozen in liquid nitrogen. RNA was extracted from liver of 23 HS rats with glucose intolerance and 23 HS rats with normal glucose. The Affymetrix 230_2 array was used to probe transcript abundance levels.

2014-09-18 | E-GEOD-54935 | biostudies-arrayexpress

Genome-wide 10K SNP profiles in heterogeneous stock rats that differ in glucose tolerance

Project description:Using heterogeneous stock (HS) rats, we have identified a region on rat chromosome 1 that maps multiple diabetic traits. We sought to use global expression analysis to determine if genes within this region are differentially expressed between HS rats with normal glucose tolerance and those with glucose intolerance HS rats were euthanized at 17 weeks of age and tail sample was taken. Genomic DNA was extracted from tail of 23 HS rats with glucose intolerance and 23 HS rats with normal glucose. The Affymetrix 10K SNP array was used to genotype these animals.

2014-09-18 | E-GEOD-57117 | biostudies-arrayexpress

Transcription profiling of mammary glands from virgin or parous Lewis strain rats

Project description:Independent Lewis rat data used to confirm the finding of the main experiment "Protection against Mammary Tumorigenesis in Multiple Rat Strains (experiment E-TABM-197: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-197).

2007-01-31 | E-TABM-198 | biostudies-arrayexpress

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