Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling of liver and white adipose tissue of male SD rats and CRISPR/Cas-9-mediated heterozygous knockout SD-Nme7+/- male rats

ABSTRACT: We aimed to compare the transcriptome of liver and white adipose tissue of adult male SD rats and the novel CRISPR/Cas-9-mediated heterozygous knockout SD-Nme7+/- adult male rats using Affymetrix Rat Gene 2.1 ST Array Strip. Total RNA was isolated from the liver and visceral adipose tissue (RNeasy Mini Kit, Qiagen) of SD and SDNme7+/- rats. The quality and integrity of the total RNA was evaluated on the Agilent 2100 Bioanalyzer system (Agilent, Palo Alto, CA). Microarray experiments were performed using the Rat Gene 2.1 ST Array Strip. The whole hybridization procedure was performed using the Affymetrix GeneAtlas® system according to the manufacturer's instructions. The quality control of the chips was performed using Affymetrix Expression Console. After applying quality filters and data normalization by the Robust Multichip Average (RMA) algorithm implemented in Affymetrix Expression Console, the set of obtained differentially expressed probesets was filtered by the false discovery rate (FDR) method implemented in PARTEK Genomics Suite 7 (Partek, St. Louis, Missouri). Transcriptomic data were then processed by a standardized sequence of analyses (hierarchical clustering and principal component analysis, gene ontology, gene set enrichment, Upstream Regulator Analysis, Mechanistic Networks, Causal Network Analysis, and Downstream Effects Analysis) using Ingenuity Pathway Analysis.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Ondřej Seda

PROVIDER: E-MTAB-10011 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of liver, pancreas and lung tissue of male SD rats and CRISPR/Cas-9-mediated knockout SD-Nme7-/- male rats

Project description:We aimed to compare the transcriptome of liver, pancreas, and lung tissue of adult male SD rats and the novel CRISPR/Cas-9-mediated knockout SD-Nme7-/- adult male rats using Affymetrix Rat Gene 2.1 ST Array Strip. Total RNA was isolated from the liver, pancreas, and lung tissues (RNeasy Mini Kit, Qiagen) of SD and SDNme7-/- rats. The quality and integrity of the total RNA was evaluated on the Agilent 2100 Bioanalyzer system (Agilent, Palo Alto, CA). Microarray experiments were performed using the Rat Gene 2.1 ST Array Strip. The whole hybridization procedure was performed using the Affymetrix GeneAtlas® system according to the manufacturer's instructions. The quality control of the chips was performed using Affymetrix Expression Console. After applying quality filters and data normalization by the Robust Multichip Average (RMA) algorithm implemented in Affymetrix Expression Console, the set of obtained differentially expressed probesets was filtered by the false discovery rate (FDR) method implemented in PARTEK Genomics Suite 7 (Partek, St. Louis, Missouri). Transcriptomic data were then processed by a standardized sequence of analyses (hierarchical clustering and principal component analysis, gene ontology, gene set enrichment, Upstream Regulator Analysis, Mechanistic Networks, Causal Network Analysis, and Downstream Effects Analysis) using Ingenuity Pathway Analysis.

2021-04-06 | E-MTAB-10000 | biostudies-arrayexpress

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

Transcriptomic profiles of white adipose tissue, brown adipose tissue and liver in rats fed either a high-fat diet or high-fat diet combined with ellagic acid treatment

Project description:In this study, we assessed the effect of acute oral administration of ellagic acid on metabolic parameters, oxidative stress and transcriptomic profiles in an inbred rodent model, carrying a variant of one of the metabolic syndrome-related genes, Zbtb16 (Zinc Finger And BTB Domain Containing 16). Over a period of three weeks, adult male rats of the SHR-Lx/k.o. strain were fed a high-fat diet accompanied with daily intragastric gavage of ellagic acid (50 mg/kg body weight; HFD-EA rats) or solvent only (HFD rats). At the end of the protocol, morphometric and metabolic parameters, including glucose tolerance test, serum lipid concentration and oxidative stress markers along with transcriptomic profile of liver, brown, and epididymal adipose tissues were assessed.

2021-02-19 | E-MTAB-8928 | biostudies-arrayexpress

Transcriptomic profiles of white adipose tissue and liver in rats fed either a high-sucrose diet or high-sucrose diet combined with quercetin treatment

Project description:Adult male rats of the PD/Cub (PD hereafter) strains were fed a laboratory chow diet (STD, ssniff RZ, ssniff Spezialdiäten GmbH, Soest, Germany). At the age of 12 months, rats within each strain were randomly divided into two groups. The control group was fed a high-sucrose diet (HSD, sucrose 70 cal%) while the experimental group was fed a HSD fortified with quercetin (10 g/kg food, Sigma-Aldrich).

2022-09-15 | E-MTAB-11061 | biostudies-arrayexpress

Gut microbiota analysis of colitic SD rats

Project description:Fecal samples collected on day 5 from randomly selected colitic SD rats were analyzed for gut microbiota by sequencing the V4 region of the 16S rRNA gene. The orally administered Dex-P-laden NPA2 coacervate (Dex-P/NPA2) significantly restores the diversity of gut microbiota compared with colitic SD rats in the Dex-P/PBS group and the untreated colitic rats (Control).

2021-11-06 | GSE167138 | GEO

The research on transcriptional profiling in plasma exosomes of SD rats: SAH vs Sham

Project description:Transcriptional profiling of plasma exosomes came from SD rats that underwent subarachnoid hemorrhage (SAH) and sham operation (Sham) rats. The goal was to identify the changes of RNA in plasma exosomes after subarachnoid hemorrhage in SD rats.

2023-10-18 | GSE230400 | GEO

Microarray expression of white adipose tissue in adult male rats treated with methylglyoxal vs. controls

Project description:In our study, we investigated the effect of methylglyoxal on metabolic, transcriptomic, metabolomic and proteomic profiles in the context of metabolic syndrome in an experimental model. Dicarbonyl stress was induced in experimental group by intragastrical administration of methylglyoxal (3x/ week in dose 0.5 mg/kg b.wt.for 4 weeks) in a strain of hereditary hypertriglyceridaemic rats (HHTg). Transcriptome assessment in white adipose tissue was performed in 7 male adult rats of experimental group and compared to that of 6 age- and sex- matched rats of control group.

2021-04-06 | E-MTAB-9013 | biostudies-arrayexpress

Microarray expression of kidney cortex in adult male rats treated with methylglyoxal vs. controls

Project description:In our study, we investigated the effect of methylglyoxal on metabolic, transcriptomic, metabolomic and proteomic profiles in the context of the development of kidney impairment in an experimental model of metabolic syndrome. Dicarbonyl stress was induced in experimental group by intragastrical administration of methylglyoxal (3x/ week in dose 0.5 mg/kg b.wt.for 4 weeks) in a strain of hereditary hypertriglyceridaemic rats (HHTg). Transcriptome assessment in kidney cortex was performed in 8 male adult rats of experimental group and compared to that of 6 age- and sex- matched rats of control group.

2020-02-08 | E-MTAB-7690 | biostudies-arrayexpress