Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans

ABSTRACT: RNA-Seq analysis was performed to assess how a glucose-supplemented diet and/or a hyl-2 mutation altered the transcriptome. Comparison analysis of transcripts associated with anoxia sensitive animals (hyl-2(tm2331) mutation or a glucose diet) revealed 199 common transcripts encoded by genes with known or predicted functions involving innate immunity, cuticle function (collagens) or xenobiotic and endobiotic phase I and II detoxification system.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE83887 | GEO | 2016/12/19

SECONDARY ACCESSION(S): PRJNA327375

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Translational profiling reveals that mRNAs encoding cuticle collagens are translationally repressed upon nsun-1 knockdown

Project description:By comparing mRNAs contained in the polysome fraction to total mRNAs in Caenorhabditis elegans exposed to either RNAi control or nsun-1 RNAi, we found that loss of NSUN-1 translationally represses genes associated with collagens, cuticle integrity and development. These changes explain phenotypes of nsun-1 depletion, which include impaired fecundity, gonad extrusion and reduced barrier function.

2020-12-09 | GSE143618 | GEO

Translational profiling reveals that mRNAs encoding cuticle collagens are translationally repressed upon nsun-1 knockdown

Project description:Translational profiling reveals that mRNAs encoding cuticle collagens are translationally repressed upon nsun-1 knockdown

| PRJNA601121 | ENA

Transcription profiling of rainbow trout cells following anoxia exposure

Project description:The rainbow trout, Oncorhynchus mykiss, is relatively sensitive to hypoxia and does not survive deep hypoxia or anoxia. Given this lack of hypoxia-tolerance in the whole animal, the aim of this experiment was to investigate the in vitro responses of cultured rainbow trout cells following anoxia exposure. Rainbow trout hypodermal fibroblast (RTHDF) cells were exposed to anoxia for 12 and 24 h, whilst control cells were held under normoxic conditions for 24 h. Differential gene expression as a consequence of the treatments was analysed using an oligoarray composed of approximately 21,500 BLAST-identified sequences fabricated on the Agilent microarray platform. 57 genes were found to display significant responses to oxygen deprivation and these genes were assigned Gene Ontology terms and IDs. Of the 57 differentially expressed genes, 6 genes associated with carbohydrate metabolism were up-regulated following anoxia, these included phosphoglucomutase (PGM) and glycogen phosphorylase, consistent with glycogen serving as an important energy source during anoxia. Other genes up-regulated in response to anoxia included a number of putative targets of hypoxia inducible factor 1 alpha (HIF1A), namely phosphoglycerate kinase, triosephosphate isomerase and the glucose transporter, GLUT2. Egl9 homolog 3, the proline hydroxylase responsible for HIF1A regulation, was also induced. This analysis indicates that cultured trout cells have the capacity for adaptive gene responses when subjected to oxygen levels that are lethal to the whole organism.

2008-06-11 | E-MAXD-41 | biostudies-arrayexpress

Timecourse of total and polysome-associated mRNA levels post glucose deprivation

Project description:Cell survival in changing environments requires appropriate regulation of gene expression, including post-transcriptional gene regulatory mechanisms. Based on reporter gene studies in glucose-starved yeast, it was proposed that translationally silenced eukaryotic mRNAs accumulate in P-bodies and can return to active translation. We present evidence contradicting the notion that this model is a widespread and general phenomenon. First, genome-wide measurements of mRNA abundance, translation, and ribosome occupancy following glucose withdrawal show that most mRNAs are lost from the cell coincident with their loss from polysomes. Second, only a very limited sub-population of translationally repressed transcripts, comprising fewer than 400 genes, can be reactivated for translation upon glucose re-addition in the absence of new transcription. This highly selective post-transcriptional regulation could be a mechanism for cells to minimize the energetic costs of reversing gene-regulatory decisions in rapidly changing environments by transiently preserving a pool of transcripts whose translation is rate-limiting for growth.

2011-09-05 | GSE31392 | GEO

Timecourse of total and polysome-associated mRNA levels post glucose deprivation

2011-09-04 | E-GEOD-31392 | biostudies-arrayexpress

The effect of in vitro cultivation on the transcriptome of adult Brugia malayi

Project description:We examined the global transcriptomic profile of B. malayi females at four different time points (6 biological replicates per time point) over 5 days in culture. Focusing on genes that are differentially expressed at various time points, we observed a general perturbation of the expression profile between dissection from the host and receipt after shipment. The expression of a few genes remained changed at the end of the experiment, after 5 days under controlled conditions; in particular, genes encoding cuticle collagens were prominently represented and strongly overexpressed.

2015-12-02 | GSE72592 | GEO

Glucose deprivation induced gene expression

Project description:Glucose deprivation induced gene expression

| PRJNA668528 | ENA

Gene expression alternations in the offspring liver from chromium restriction diet dams

Project description:Maternal chromium restriction may disturb susceptibility in offspring. Liver from maternal chromium diet has 264 up- and 199 down- regulated genes, compared to control. Especially, Insulin signaling pathway and WNT pathway were affected.

2017-02-08 | GSE82028 | GEO

Glucose deprivation induced gene expression

Project description:Glucose is the main substrates of cancer cell metabolism. Relying on glucose for rapid proliferation and maintaining intracellular redox homeostasis is one of the hallmarkers of cancer cells. During physiology or cancer treatment, cancer cells will face a limited supply of glucose. In these case, cancer cells will undergo cell death . The plasticity of cancer cells is the main factor that allows cancer cells to survive this difficult situation. So in order to better understand the cplasticity of cancer cells, we use glucose-free medium to treat the colorectal cancer cell line HCT116, and perform RNA-Seq analysis on the treated samples.

2021-05-01 | GSE159351 | GEO

Effect of Hyp, low phosphate diet and sex on mRNA gene expression in the mouse kidney

Project description:The renal adaptation to changing dietary phosphate levels is not well understood. The dominant Hyp mutation of the Phex gene in mice causes X-linked hypophosphatemia with low renal retention of phosphate and blocks physiologic adaptation to low phosphate diets. At P < 0.01, there were 1,711 transcripts significantly affected by genotype, 1,428 by diet and 5,601 by sex. Many renal transporters other than phosphate, as well as many novel transcripts of unknown function, were affected by the Hyp mutation. Some genes for fat metabolism and inflammation were up-regulated in Hyp kidneys. Of the genes affected by genotype and diet, only 378 were affected by both. In summary, the Hyp mutation induced changes in mRNA levels for numerous transcripts exceeding that required to alter phosphate retention. The data suggest broader physiological roles for the Phex gene unrelated to phosphate conservation. Keyword = Phex Keyword = Hyp Keyword = mouse Keyword = kidney Keyword = sex Keyword = mRNA Keyword = microarray Keyword = low phosphorus diet Keywords: disease state analysis

2007-01-01 | GSE5243 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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