Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of C. elegans wildtype and gas-1 mitochondrial mutants

ABSTRACT: Utilizing C. elegans as a model of mitochondrial dysfunction provides insight into cellular adaptations which occur as a consequence of genetic alterations causative of human disease. We characterized genome-wide expression profiles of hypomorhpic C. elegans mutants in nuclear-encoded subunits of respiratory chain complexes I, II and III. Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways utilizing gene set enrichment analysis. Experiment Overall Design: 5 biological replicates of wildtype and electron transport chain (ETC) mutant C. elegans were used as sources of total RNA, each for hybridization to a single Affymetrix whole-genome microarray. Comparison of the data was intended to reveal metabolic pathways downstream of the mutation.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Marni Falk

PROVIDER: E-GEOD-9896 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of C. elegans complex RNAi mutant vs wildtype

Project description:This SuperSeries is composed of the following subset Series:; GSE9896: Expression data from wildtype and gas-1 mitochondrial mutant C. elegans; GSE9897: Expression data from 2 wildtype and 8 C. elegans ETC mutants Experiment Overall Design: Refer to individual Series

2008-04-08 | E-GEOD-9967 | biostudies-arrayexpress

Transcription profiling from C. elegans ETC mutants vs. Wildtypes

Project description:Utilizing C. elegans as a model of mitochondrial dysfunction provides insight into cellular adaptations which occur as a consequence of genetic alterations causative of human disease. We characterized genome-wide expression profiles of hypomorphic C. ele; Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways utilizing gene set enrichment analysis. Experiment Overall Design: 3 biological replicates of each C. elegans strain were used as sources of total RNA combined for hybridization to a single Affymetrix whole-genome microarray. Comparison of the data was intended to reveal metabolic pathways downstream of the mutation.

2008-04-08 | E-GEOD-9897 | biostudies-arrayexpress

NAD+ and PPAR-modifying drugs in a C. elegans model of respiratory chain complex I deficiency

Project description:The gas-1(fc21) mutation affects the 49 kD subunit of complex I, decreasing the rate of complex I-dependent oxidative phosphorylation. This is a model for human mitochondrial respiratory chain disease. NAD+ and PPAR-modifying drugs may confer benefits with respect to lifespan in these short-lived mutant worms. Analysis of gas-1(fc21) electron transport chain complex I mutants treated either starting in development or in young adulthood only with nicotinic acid (1 mM), resveratrol (50 microM), rosiglitazone (5 mM) or fenofibrate (14 microM) is presented. The goal is to detect transcriptional changes in clusters of genes using gene set enrichment analysis to explain treament effects in these mutant worms. Four biological replicates were performed for each treatment condition (nicotinic acid, resveratrol, rosiglitazone, and fenofibrate) for each drug beginning either in development or in young adulthood for gas-1 mutant worms, i.e., 8 treated samples in total. At most one outlier was excluded from each analysis. Untreated N2 and gas-1 in each of the control solvents (S-basal, for nicotinic acid, and 1% DMSO, for resveratrol, rosiglitazone, and fenofibrate) were also analyzed; at least 3 replicates of each were included. These were used as sources of total RNA, each for hybridization to a single Affymetrix whole-genome microarray. Analysis was performed to reveal transcriptional changes related to mutantion and/or drug treatment effects.

2014-08-13 | E-GEOD-57626 | biostudies-arrayexpress

Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans

Project description:This SuperSeries is composed of the following subset Series: GSE21008: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans: atrazine GSE21010: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans: cadmium GSE21011: Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans: fluoranthene Refer to individual Series

2010-03-23 | E-GEOD-21012 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development [RNA-seq for polyA enriched mRNAs]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of three timecourses that were collected over C. elegans development and analyzed by RNA-seq of mRNA libraries

2014-03-01 | E-GEOD-52861 | biostudies-arrayexpress

Expression analysis of Caenorhabditis elegans Bristol N2 rsd-2 and rsd-6 single mutants at 25Â°C and 20Â°C

Project description:Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 rsd-2 and Bristol N2 rsd-6 single mutants, compared to late-generation strains at 25Â°C and 20Â°C A six chip study using total RNA recovered from two separate alleles of Caenorhabditis elegans Bristol N2 rsd-2 and one allele Bristol N2 rsd-6 , in which the effects of transgeneration aging are studied in early generation animals and late generation animals at the restrictive temperature of 25Â°C and the permissive temperature, 20Â°C.

2013-06-01 | E-GEOD-40459 | biostudies-arrayexpress

Developmental Timecourses total-RNA sequencing [Ribosome repleted total RNA]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Examination of two timecourses that were collected over C. elegans development and analyzed by RNA-seq of "RiboMinus" libraries

2014-03-01 | E-GEOD-52864 | biostudies-arrayexpress

A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence

Project description:Pseudomonas aeruginosa is an opportunistic pathogen that causes severe health problems. Despite intensive investigation, many aspects of microbial virulence remain poorly understood. We used a high-throughput, high-content, whole-organism, phenotypic screen to identify small molecules that inhibit P. aeruginosa virulence in C. elegans. Approximately half of the hits were known antimicrobials. A large number of hits were non-antimicrobial bioactive compounds, including the cancer chemotherapeutic 5-fluorouracil. We determined that 5-fluorouracil both transiently inhibits bacterial growth and reduces pyoverdine biosynthesis. Pyoverdine is a siderophore that regulates the expression of several virulence determinants and is critical for pathogenesis in mammals. We show that 5-fluorouridine, a downstream metabolite of 5-fluorouracil, is responsible for inhibiting pyoverdine biosynthesis. We also show that 5-fluorouridine, in contrast to 5-fluorouracil, is a genuine anti-virulent compound, with no bacteriostatic or bacteriocidal activity. To our knowledge, this is the first report utilizing a whole-organism screen to identify novel compounds with antivirulent properties effective against P. aeruginosa. There are 6 samples total that comprise three biological replicates of N2 animals exposed to DMSO or 5-fluorouracil for 8 hours at 25Â°C. Each biological replicate consists of N2 C. elegans animals in the young adult developmental stage.

2016-08-10 | E-GEOD-85342 | biostudies-arrayexpress

Caenorhabditis sex-specific RNAseq

Project description:This project defines the transcriptomes of XO (male) and XX (female or mutant pseudo-female) Caenorhabditis nematodes. The data allow the overall composition and sexual regulation of the transcriptome within a single species to be determined. In addition, the five related species studied allow meta-comparisons between them. Because two of the five (C. elegans and C. briggsae) produce a self-fertile XX hermaphrodite, while the XX sex in the remaining three (C. japonica, C. remanei, and C. brenneri) are true females, the data are particularly useful for inferring effects of sexual mode on genome-wide gene expression. L4 larvae and adults were pooled for each sex for five species (C. elegans, C. briggsae, C. japonica, C. brenneri, and C. remanei). Each of these 10 species-sex combinations was replicated three times, for a total of 30 samples.

2012-10-25 | E-GEOD-41367 | biostudies-arrayexpress

Transcription profiling by array of C. elegans exposed to quercetin and tannic acid

Project description:Recent research has highlighted that the polyphenols Quercetin (Q) and Tannic acid (TA) are capable of extending the lifespan of C. elegans. To gain a deep understanding of the underlying molecular genetics, we analyzed the global transcriptional patterns of nematodes exposed to Quercetin or Tannic acid concentrations that are non-effective (in lifespan extension), lifespan extending or toxic. The global transcriptome was compared in wild type nematodes raised in the presence of 0, 50, 100, and 200 µM Quercetin (Q) or 0, 100, 200, and 300 µM Tannic acid (TA).

2012-02-03 | E-GEOD-35354 | biostudies-arrayexpress

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