Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

To identify differentially expressed genes in ventricular tissue between wildtype control and the 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish at six months.

ABSTRACT: To identify differentially expressed genes in ventricular tissue between wildtype control and the 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish at six months.

PROVIDER: PRJNA1123307 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR29382474_1.fastq.gz	Fastqsanger.gz
	SRR29382474_2.fastq.gz	Fastqsanger.gz
	SRR29382476_1.fastq.gz	Fastqsanger.gz
	SRR29382476_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

To identify differentially expressed genes in ventricular tissue between wildtype control and the 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish at six months.

Project description:To seek molecular mechanisms underlying the mechanisms of mutant genotypes by comparing them witht he wild types, we performed whole transcriptome RNA-sequencing experiments using ventricular tissue isolated from 6-month-old mtorxu015/+ mutant, Tg(cmlc2:tfeb) transgenic zebrafish,and corresponding WT siblings.

2025-06-12 | GSE269725 | GEO

Identification of TFEB regulated genes during in vitro RGC to EPC differentiation (RNA-seq)

Project description:The largest germinal niche of the adult mammal brain locates at the ventricular zone (VZ), which is made up of adult neural stem cells (NSCs) and multiciliated ependymal cells (EPCs). Both NSCs and EPCs derive from radial glia (RG), whereas the transcriptomic dynamic changes of the cell fate continuum remain elusive. Here, we identified a key transcription factor TFEB that is important during EPC differentiation. We knockdown TFEB using siRNA and check gene expression changes upon TFEB depletion by RNA-seq.

2024-04-21 | E-MTAB-13856 | biostudies-arrayexpress

TFEB activation in macrophages attenuates postmyocardial infarction ventricular dysfunction independently of ATG5-mediated autophagy

Project description:Lysosomes are at the epicenter of cellular processes critical for inflammasome activation in macrophages, including autophagy and lipid metabolism. Inflammasome activation and IL1-beta secretion are implicated in atherogenesis, ischemic cardiac injury and resultant heart failure; however, little is known about the role of macrophage lysosome function in regulating these processes. We hypothesized that macrophages exhibit lysosome dysfunction in heart failure due to ischemic injury, and that augmentation of macrophage lysosomal biogenesis via macrophage-specific overexpression of transcription factor EB (mf-TFEB) would attenuate ischemic remodeling by modulating macrophage inflammatory responses. In both mice subject to ischemia-reperfusion injury, and human heart tissue from patients with ischemic cardiomyopathy, we find evidence of lysosome insufficiency and autophagic impairment, respectively. Mf-TFEB overexpression significantly attenuated post-IR adverse left ventricular remodeling at 4 weeks without affecting scar size. Mf-TFEB overexpression reduced the relative amounts of pro-inflammatory macrophage populations in the myocardium. RNA sequencing of flow-sorted cardiac macrophages post-IR confirmed that TFEB stimulated a lysosomal transcriptional program in macrophages, and upregulated key targets involved in lysosomal lipid metabolism, which we show are critical for inflammasome suppression. Both TFEB-dependent inflammasome suppression and effects on post-IR remodeling were independent of autophagy. Our findings suggest that TFEB reprograms macrophage lysosomal lipid metabolism to attenuate inflammasome activity and protect against post-ischemic cardiac remodeling and simultaneously shift our understanding of how autophagy and lipid metabolism impact acute inflammation.

2019-11-01 | GSE118463 | GEO

Obesity impact on the left ventricular transcriptome of 4 and 10 months old SHHF rats

Project description:Impact of the obesity on RNA total levels of male SHHF left ventricular aged from 4 and 10 months old. Keywords: Comparative cDNA hybridization

2006-07-05 | GSE2876 | GEO

Feeding activates FGF15-SHP-TFEB-mediated lipophagy in the gut

Project description:Lysosome-mediated macroautophagy, including lipophagy, is activated under nutrient deprivation but is repressed after feeding. We show that feeding unexpectedly activates intestinal lipophagy in a manner dependent on both the orphan nuclear receptor, small heterodimer partner (SHP/NR0B2), and the late fed-state gut hormone, fibroblast growth factor-15/19 (FGF15/19). Postprandial intestinal triglycerides (TGs) and apolipoprotein-B48 (ApoB48), the TG-rich chylomicron marker, were elevated in SHP-knockout and FGF15-knockout mice. Genomic analyses in mouse intestine revealed that SHP partners with the key lysosomal activator, transcription factor-EB (TFEB), upregulating autophagy/lipolysis network genes after feeding. In HT29 intestinal cells, FGF19 treatment activated lipophagy in a manner dependent on both SHP and TFEB, reducing TG and ApoB48 levels. Mechanistically, feeding-induced FGF15/19 signaling increases nuclear localization of TFEB and SHP via PKCβ/ζ-mediated phosphorylation, leading to transcriptional induction of Ulk1 and Atgl. Collectively, these results demonstrate that after feeding, FGF15/19-activated SHP and TFEB paradoxically activate gut lipophagy, limiting postprandial TG levels. As excess lipids cause dyslipidemia and obesity, the FGF15/19-SHP-TFEB axis that reduces intestinal TGs via lipophagic activation provides promising therapeutic targets for obesity-associated metabolic disease.

2022-04-22 | GSE197549 | GEO

Genome-wide Binding sites of TFEB during in vitro RGC to EPC differentiation (ChIP-seq)

Project description:The largest germinal niche of the adult mammal brain locates at the ventricular zone (VZ), which is made up of adult neural stem cells (NSCs) and multiciliated ependymal cells (EPCs). Both NSCs and EPCs derive from radial glia (RG), whereas the transcriptomic dynamic changes of the cell fate continuum remain elusive. Here, we used TFEB ChIP-seq to investigate its role in during EPC differentiation.

2024-04-21 | E-MTAB-13855 | biostudies-arrayexpress

Cardiac transcriptome analysis of right and left ventricular heart specimens of BBLN-transgenic mice by NGS

Project description:The study performed NGS to investigate the cardiac transcriptomes of right and left ventricular heart specimens of 3-4-month-old BBLN-transgenic mice with FVB/N background in comparison to those of non-transgenic FVB/N mice. BBLN-transgenic (Tg-BBLN) mice with myocardium-specific BBLN expression were generated to investigate the cardiac phenotype of increased cardiac BBLN transcript levels because the function of BBLN (Bublin coiled-coil protein), which is the chromosome 9 open reading frame(C9orf16), is largely unknown. Tg-BBLN mice with increased cardiac BBLN levels developed features of heart failure with increasing age. Pathomechanisms of heart failure induced by BBLN were investigated by NGS of right and left ventricular heart specimens of male, BBLN-transgenic mice (age: 3-4 months). NGS data reveal transcriptome changes in right and left ventricular heart specimens induced by increased expression of BBLN in the heart.

2023-09-18 | GSE241022 | GEO

Transcription profiling of rat left ventricular samples from 12-, 16- and 20-month old spontaneously hypertensive rats (SHRs) compared with age-matched Wistar-Kyoto (WKY) rats as controls

Project description:Left ventricular gene expression profiles from 12-, 16- and 20-months old spontaneously hypertensive rats (SHRs) were compared with left ventricular profiles seen in age-matched Wistar-Kyoto (WKY) rats [control rats] by screening Affymetrix U34A arrays (there are 4 samples in each timepoint except 3 samples of 20-months old WKYs).

2007-09-20 | E-GEOD-2116 | biostudies-arrayexpress

TFEB activation in macrophages attenuates postmyocardial infarction ventricular dysfunction independently of ATG5-mediated autophagy

Project description:TFEB activation in macrophages attenuates postmyocardial infarction ventricular dysfunction independently of ATG5-mediated autophagy

| PRJNA485726 | ENA

Expression data from injected mice overexpressing TFEB specifically in liver

Project description:In order to identify the effects of transcription factor EB (TFEB) overexpression on the liver transcriptome, we performed Affymetrix GeneChip hybridization experiments on injected mice overexpressing TFEB specifically in the liver. For the analysis of the injected mice overexpressing TFEB, total RNA was extracted from the liver of three mice. RNA extracted from the liver of 3 not-injected mice was used as a control.

2013-04-20 | E-GEOD-35015 | biostudies-arrayexpress

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