Decorin protects cardiac myocytes against simulated ischemia/reperfusion injury
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 550
ORGANISM(S): Rattus norvegicus
SUBMITTER: Kamilla Gömöri
PROVIDER: E-MTAB-9325 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The aim of the experiment was the analysis of key molecular changes with an unbiased, transcriptomics-based approach in a prediabetes model. Small RNA sequencing analysis was applied to explore the expression changes resulted high-fat chow (supplemented with 40% lard) diet for 21 weeks and a single low dose of streptozotocin (20 mg/kg) treatment at week 4. Long-Evans rats were used in the present study. Left ventricular samples(n=6) of both prediabetic and control groups were analyzed.
2020-04-24 | E-MTAB-8204 | biostudies-arrayexpress
Project description:The aim of the experiment was to analyze key molecular changes using an unbiased, transcript-based approach in an experimental obesity model. Small expression RNA sequencing analysis was used to reveal expression changes. Male Long-Evans rats were given a control (CON) or high fat (20%) high sucrose (15%) diet (HFS) for 25 weeks. From week 16, the animals were injected. 0.25 mg · kg - 1 daily with selegiline (CON + S and HFS + S) or vehicle (CON, HFS). Left ventricular samples from all four groups (n = 4-5) were analyzed.
2022-09-30 | E-MTAB-10191 | biostudies-arrayexpress
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2021-10-06 | E-MTAB-10720 | biostudies-arrayexpress
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2022-01-04 | E-MTAB-10912 | biostudies-arrayexpress
Project description:The aim of this study was to compare the most common immortalized cardiac cell lines (human: AC16, rat: H9C2, mouse: HL-1) to primary cultures (neonatal rat or mouse cardiomyocytes, and human induced pluripotent stem cells) and left ventricular tissues from the corresponding species. To characterize cardiac cell lines, cardiac cell lines were seeded onto plates, and their differentiation towards a more cardiac phenotype was induced on the basis of most commonly used protocols in literature. The cells were harvested either in stage of proliferation or differentiation, and left ventricular tissue from each corresponding species, and isolated neonatal primary cardiac myocytes (for mouse and rat) or human induced pluripotent stem cells were applied as references for comparison. Transcriptomic analysis was performed on all samples. Generally, the mRNA expression pattern of cardiac markers in the cell lines showed significant differences compared to corresponding tissue or primary cultures. mRNA profile of cell lines indicates poor cardiac characteristics regardless the differentiation protocol used. Limitations of these cell lines should be taken into account when these cells are used as in vitro platforms to model cardiomyocytes and cardiovascular diseases.
2022-01-04 | E-MTAB-10913 | biostudies-arrayexpress
Project description:Mechanical loading is a key determinant of bone mass, geometry and strength and is essential to maintain optimal skeletal health. We hypothesized that spontaneous low-impact exercise would affect global gene transcript levels in cortical bone of growing rats. We used RNA-Seq to analyse the transcriptome of the femoral mid-diaphysis in pre-pubertal male rats that were assigned to one of three exercise groups for 15 days: control (CON); bipedal stance (BPS); and wheel exercise (WEX). RNA-seq analysis identified 808 and 324 differentially expressed transcripts in the BPS and WEX animals, respectively. In WEX animals, the up-regulated transcripts were enriched for gene ontology terms associated with bone metabolism. Both BPS and WEX animals showed changes in transcripts that were enriched for muscle-related processes. However, in WEX these transcripts were down-regulated while in BPS such transcripts were up-regulated. Importantly, we observed that the exercise mode had diametrically opposite effects on transcripts for multiple genes within the integrin-linked kinase (ILK) and Ca2+ signalling pathways such that they were up-regulated in BPS and down-regulated in WEX. The findings are important for our understanding of possible ways in which different exercise regimens might affect bone when normal activities apply mechanical stimuli during post-natal growth and development. 24 weanling (21 day old) male Sprague-Dawley rats were assigned to three exercise groups .After the 15 day trial period, total RNA was extracted from the femoral diaphysis and mRNA profiles were analysed using RNA-seq
2015-11-02 | E-GEOD-67787 | biostudies-arrayexpress
Project description:We found that cardiac fibroblasts produce and secrete exosomes. miRNA profiling and TaqMan qRT-PCR experiments identified miR-21 expression to be higher in cardiac fibroblasts compared to those of miR-21*, whereas in exosomes miR-21* expression was higher compared to miR-21. The purpose of the study was to validate these findings by miRNA sequencing in cardiac fibroblasts and fibroblasts-derived exosomes. Neonatal rat cardiac fibroblasts were cultured in DMEM + 1% exosome-depleted FBS for 48h. Conditioned medium was collected and exosomes were purified by several centrifugation and filtration steps, following ultracentrifugation. Afterwards total RNA from cardiac fibroblasts and exosomes was isolated for miRNA sequencing.
2015-12-19 | E-GEOD-76175 | biostudies-arrayexpress
Project description:2nd generation sequencing was used to compare expression profiles of MBP-specific T cells retrieved from blood, CSF, spinal cord meninges and parenchyma. The overall expression profiles were found to be very similar.However, genes regulated during T cell activation were found to be upregulated in T cells from spinal cord meninges and parenchyma compared to blood and CSF. 2nd generation sequencing of MBP-specific T cells retrieved from blood and CNS compartments during experimental autoimmune encephalomyelitis
2016-02-12 | E-GEOD-75488 | biostudies-arrayexpress
Project description:ChIP-seq of H3K4me3 in rat peripheral nerve was used to identify transcription start sites associated with Schwann cell-expressed genes. The analysis was performed in injured and control nerve to identify injury-responsive changes in Schwann cells. H3K4me3 ChIP samples were prepared from rat sciatic nerve at 1 day post-transection using both the distal stump of the injured nerve and the contralateral (sham) nerve.
2016-08-01 | E-GEOD-84272 | biostudies-arrayexpress
Project description:We report on the characterization of lipogenic tissue transcriptional networks that support physiological responses of obese rats to a lipid-lowering bioactive food compound, R-a-lipoic acid (LA). Nine-week old male ZDF (fa/fa) rats were fed a chow diet supplemented with 3 g LA per kg diet or pair fed for two weeks. At the end of the trial, high-quality RNA was extracted from the liver and epididymal fat and subjected to transcriptome analysis using RNA-Seq technology. Results showed a substantially higher number of differentially expressed genes (DEG, q ⤠0.05 and absolute log2(fold change) ⥠1) in liver (110 genes) vs. epididymal fat (10 genes). Most epididymal fat DEG were also differentially expressed in liver and shared directionality of change. Gene Ontology (GO) analysis of these transcripts revealed significant enrichment of GO categories related to immune response, stress response, lipid metabolism, and carboxylic acid metabolic processes. Of interest interferon-related genes involved in defense against microorganism and innate immune response were induced by LA. Lipid metabolism-related transcript changes observed in LA-fed animals included downregulation of lipogenic genes (Pnpla3, Pnpla5, Elov6, Acly, Gpam, and Aacs) and concomitant upregulation of short-, medium- and long-chain fatty acid metabolic processes (Acot1, Acot2, Acsf2, and Crat). Transcriptional changes were accompanied by the lowering of abdominal adiposity and blood triacylglycerol levels. We conclude that LA dietary supplementation induces prominent gene expression changes in liver in support of significant improvement of whole-body lipid status For each tissue and feed combination (liver/LA+, liver/LA-, adipose/LA+, and adipose/LA-) the transcriptome was sequenced with 4 biological replicates.
2014-01-08 | E-GEOD-50424 | biostudies-arrayexpress