Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rattus norvegicus

ABSTRACT: Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat

PROVIDER: PRJNA215848 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR954775_1.fastq.gz	Fastqsanger.gz
	SRR954775_2.fastq.gz	Fastqsanger.gz
	SRR954776_1.fastq.gz	Fastqsanger.gz
	SRR954776_2.fastq.gz	Fastqsanger.gz
	SRR954777_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 96

Similar Datasets

Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat

Project description:The metabolic syndrome (MetS) is a collection of co-occurring complex disorders including obesity, hypertension, dyslipidemia, and insulin resistance. The Lyon Hypertensive (LH) and Lyon Normotensive (LN) rats are models of MetS sensitivity and resistance, respectively. To identify genetic determinants and mechanisms underlying MetS, 169 rats from an F2 intercross between LH and LN were studied. Multi-dimensional data were obtained including genotypes of 1536 SNPs, 23 physiological traits including blood pressure, plasma lipid and leptin levels, and body weight/adiposity, and more than 150 billion nucleotides of RNA-seq reads from the livers of 36 F2 individuals, 6 LH and 6 LN individuals. We identified 17 pQTLs (physiological quantitative trait loci) and 1200 eQTLs (gene expression quantitative trait loci). Systems biology methods were applied to identify 18 candidate MetS genes, including genes (Prcp and Aqp11) previously shown to be MetS-related. We found an eQTL hotspot on RNO17, which was also located within pQTLs for MetS-related traits. The genes regulated by this eQTL hotspot were mainly in two co-expression network modules (a mitochondria related module and a gene regulation related module) and were predicted to causally affect many MetS-related traits. Multiple evidences strongly and consistently support RGD1562963, a gene regulated in cis by this eQTL hotspot and possibly related to RNA stability, as the eQTL driver gene directly affected by genetic variation between LH and LN rats; the expression of this gene is also correlated with MetS-related traits. Our study sheds light on the intricate pathogenesis of MetS and proved that systems biology with high-throughput sequencing is a powerful method to study the etiology of complicated diseases. RNA-Seq of the liver of 6 LH (Lyon Hypertensive) rats and 6 LN (Lyon Normotensive) rats and 36 F2 rats.

2014-10-31 | E-GEOD-50027 | biostudies-arrayexpress

Fumaric acid esters can block pro-inflammatory actions of human CRP and ameliorate metabolic disturbances in transgenic spontaneously hypertensive rats

Project description:Inflammation and oxidative stress have been implicated in the pathogenesis of metabolic disturbances. Esters of fumaric acid, mainly dimethyl fumarate (DMF), exhibit immunomodulatory, anti-inflammatory, and anti-oxidative effects. In the current study, we tested the hypothesis that fumaric acid ester treatment of an animal model of inflammation and metabolic syndrome, the spontaneously hypertensive rat transgenically expressing human C-reactive protein (SHR-CRP), will ameliorate inflammation, oxidative stress, and metabolic disturbances.

2015-12-31 | E-MTAB-2406 | biostudies-arrayexpress

Transcriptomic landscape and metabolic phenotypization of Polydactylous rat with metabolic syndrome after high fat diet challenge

Project description:Metabolic syndrome, with its ever-rising incidence, is an important cause of worldwide morbidity and mortality. MetS is diagnosed if three or more of the following criteria are met: obesity, high serum triglycerides, low HDL-cholesterol, high blood pressure and high serum glucose. Metabolic syndrome has a complex pathogenesis which includes on one hand sedentary lifestyle and high caloric intake, on the other hand there is clear genetic predisposition with heritability in the range of 0.25-0.8. Polydactylous rat (PD hereafter) is a rodent model of metabolic syndrome manifesting dyslipidemia, insulin resistance and obesity without hypertension. To unravel the genetic and pathophysiologic background of this phenotype we compared liver transcriptomes as well as morphometric and metabolic parameters (lipidemic profiles and serum markers) among PD, Spontaneously hypertensive rat and Brown Norway rat lines after high fat diet challenge. We used microarray aproach to unravel gene expression differences between SHR, PD and BN responsible for the different phenotypes in our rat strains.

2021-06-03 | GSE164176 | GEO

Microarray expression of white adipose tissue, brown adipose tissue and liver in adult rat offspring of dams fed high-sucrose diet vs. standard diet

Project description:We established a new minimal congenic rat strain containing only a single gene, Zbtb16, from a metabolic syndrome model, the polydactylous rat (PD/Cub) strain, within the spontaneously hypertensive rat (SHR) strain genomic background. 16-week-old SHR and SHR-Zbtb16 rat dams were fed either standard diet during pregnancy and 4 weeks of lactation (control groups) or a high-sucrose diet (HSD, 70% calories as sucrose) during the same period. We have compared the transcriptome profile (GeneChip Rat Gene 2.1 ST Array Strip) in liver, brown and white adipose tissue in adult male offspring of SHR and SHR-Zbtb16 rat dams.

2019-06-28 | E-MTAB-6838 | biostudies-arrayexpress

Expression data from liver tissue from Spontaneously hypertensive rat (SHR) and its minimal congenic strain PD5 on standart labaratory chow and after dexamethasone challenge

Project description:The dissection of genetic components of metabolic syndrome is currently one of the most important research topics. Plzf gene is a promising candidate gene. Previously, we described minimal congenic strain PD5 derived from spontaneously hypertensive rat (SHR), containing congenic segment of polydactylous (PD/Cub) origin with a 2964bp intronic deletion within Plzf gene and displaying attenuated features of metabolic syndrome. To unravel the genetic background responsible for the observed of this phenotype in PD5 we compared liver transcriptomes and physiologic parameters between SHR and PD5 strains without intervention and after dexamethasone administration.

2024-09-28 | GSE234984 | GEO

Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat

2014-10-31 | GSE50027 | GEO

Transcription profiling of peritoneal fat of SHR/01a (spontaneously hypertensive rat), BN-Lx (Brown Norway congenic carrying polydactyly-luxate syndrome)and recombinant inbred (HXB/BXH) 6-week old rat strains

Project description:Gene expression profiling of peritoneal fat of SHR/01a (spontaneously hypertensive rat), BN-Lx (Brown Norway congenic carrying polydactyly-luxate syndrome)and recombinant inbred (HXB/BXH) 6-week old rat strains.

2010-11-18 | E-AFMX-7 | biostudies-arrayexpress

Gene expression in rat ovaries treated with DHT

Project description:Polycystic ovarian syndrome (PCOS) is an endocrine disorder of the reproductive and metabolic axis in women during the reproductive age. In this study, we used a rat model exhibiting reproductive and metabolic abnormalities similar to human PCOS to unravel the molecular mechanisms underlining this complex syndrome.

2016-01-01 | GSE59456 | GEO

Differential gene expression in the stellate ganglia of 16 week wistar and spontaneously hypertensive rat samples

Project description:Hypertension remains a poorly understood condition, and the understanding of the sympathetic nervous systems role in this disease remains even more limited. In this study, RNA-sequencing is used to identify transcriptomal differences in the sympathetic stellate ganglia between the 16-week-old normotensive wistar strain and the spontaneously hypertensive rat strain.This dataset should allow for further molecular characterisation of hypertensive changes in a cardiac-innervating sympathetic ganglion.

2018-06-21 | GSE110197 | GEO

Spontaneous nonsense mutation in Tuft1 (tuftelin 1) gene is associated with abnormal hair appearance and amelioration of glucose and lipid metabolism in the rat

Project description:A new spontaneous mutation, abnormal hair appearance in the rat, has been identified as a non-functional Tuft1 (tuftelin 1) gene. The pleiotropic effects of this mutation regulate glucose and lipid metabolism. Analysis of the liver proteome revealed possible molecular mechanisms for the metabolic effects of the Tuft1 gene. Recently, we identified a recessive mutation, an abnormal coat appearance, in BXH6 strain, a member of the HXB/BXH set of recombinant inbred strains derived from the SHR (spontaneously hypertensive rat) and BN-Lx (Brown Norway rat) progenitors. Whole genome sequencing of the mutant rats identified the 195875980 G/A mutation in the Tuft1 (tuftelin 1) gene on chromosome 2, which resulted in a premature stop codon. Compared to wild-type BXH6 rats, BXH6-Tuft1 mutant rats exhibited lower body weight due to reduced visceral fat and ectopic fat accumulation in the liver and heart. Reduced adiposity was associated with decreased serum glucose and insulin, and increased insulin-stimulated glycogenesis in skeletal muscle. In addition, mutant rats had lower serum MCP-1 and leptin levels, indicative of reduced inflammation. Analysis of the liver proteome identified differentially expressed proteins from fatty acid metabolism and beta oxidation, peroxisomes, carbohydrate metabolism, inflammation, and proteasome pathways. These results provide evidence for an important role of Tuft1 gene in the regulation of lipid and glucose metabolism and suggest underlying molecular mechanisms.

2024-03-12 | PXD045880 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data