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Transcription profiling of C. elegans complex RNAi mutant vs wildtype

ABSTRACT: 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

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Marni Falk

PROVIDER: E-GEOD-9967 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

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 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.

2008-04-07 | E-GEOD-9896 | 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

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

Micro-proteomics with iterative data analysis: proteome analysis in C. elegans at the single worm level

Project description:Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of C. elegans, a eukaryote composed of 959 somatic cells and ~1,500 germ cells, measuring the worm proteome at a single organism level to a depth of ~ 3,000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (> 6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource.

2015-11-17 | PXD002948 | Pride

Quantitative temporal phosphoproteomics of aging C.elegans under different environmental temperatures

Project description:Temperature is one of the primary environmental factors that affect aging, in which protein phosphorylation is an important regulator. Currently, the understanding of phosphorylation events in regulatory networks during aging has remained rather limited. Therefore, the phosphoproteomes of C.elegans of different age groups cultured at 20°C in natural aging process and 25°C in accelerated aging process were analyzed. Through using the iTRAQ-labeled phosphoproteomics method, 2375 phosphoproteins and 9063 phosphosites were identified. Volcano plots illustrated that 208 proteins during natural aging and 130 during accelerated aging, were significantly changed. Gene ontology and pathway analysis revealed that these proteins were mainly involved in temperature response, DNA transcription, protein translation, tissue system development and animal behavior processes. Moreover, our results uncovered those kinases CK2, MAPK and CAMK2 might play important roles in aging regulation. In summary, our results provided a new insight into the complicated phosphor-regulatory network system during aging and an important resource for future studies of protein phosphorylation in worms.

2018-08-08 | PXD009661 | Pride

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

Genome-wide expression analysis during aging in C. elegans

Project description:Aging has been shown to be under genetic control in C. elegans. We performed Affymetrix micorarray-based transcriptional profililng of wild type C. elegans strain Bristol N2 during aging to detect temporal changes in gene expression. RNA was prepared for hybridization to Affy microarrays from synchronized populations of C. elegans at three points during aging: 1) the late larval L4 stage, 2) day 6 of adulthood, and 3) day 15 of adulthood.

2011-05-11 | E-GEOD-21784 | biostudies-arrayexpress

RSD-2 and RSD-6 promote germ cell immortality by repressing spermatogenesis and repeat loci via small interfering RNAs

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-06-01 | E-GEOD-40460 | 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

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

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