Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA microarray analysis on young adult Caenorhabditis elegans exposed to benzene, toluene, formaldehyde and a BTF mix

ABSTRACT: In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to three chemicals (benzene (B), toluene (T), formaldehyde (F)) individually and as a BTF mix on the soil nematode, Caenorhabditis elegans. We performed whole genome DNA microarray experiments with subsequent quantitative analysis conducted on selected genes. We used synchronized C. elegans populations exposed to B, T, F or a BTF mix, and whole genome microarrays to screen for global changes in C. elegans transcription profiles. Young adults of C. elegans were selected for RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: jinhee choi

PROVIDER: E-GEOD-23013 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

mRNA microarray analysis on young adult Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio exposed to benzene, toluene, and formaldehyde

Project description:This SuperSeries is composed of the following subset Series: GSE23013: mRNA microarray analysis on young adult Caenorhabditis elegans exposed to benzene, toluene, formaldehyde and a BTF mix GSE24845: mRNA microarray analysis on young adult Drosophila exposed to benzene, toluene, and formaldehyde GSE24846: mRNA microarray analysis on young adult zebrafish exposed to benzene, toluene, formaldehyde and a BTF mix Refer to individual Series

2011-12-31 | E-GEOD-24923 | biostudies-arrayexpress

mRNA microarray analysis on young adult Caenorhabditis elegans exposed to MWCNT

Project description:In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to multiwall carbon nanotube (MWCNT) on the soil nematode, Caenorhabditis elegans. We performed whole genome DNA microarray experiments with subsequent quantitative analysis conducted on selected genes. We used synchronized C. elegans populations exposed to MWCNT for 4 and 24h, and whole genome microarrays to screen for global changes in C. elegans transcription profiles. Young adults of C.elegans were selected for RNA extraction and hybridization on Affymetrix microarrays.

2011-12-31 | E-GEOD-24847 | biostudies-arrayexpress

Transcription profiling of Caenorhabditis elegans to investigate the ecotoxicity of silver nanoparticles on the soil nematode using functional ecotoxicogenomics

Project description:Gene expression analysis was conducted on the wildtype Caenorhabditis elegans exposed to silver nanoparticles (AgNPs) using whole genome microarray. Differentially expressed genes from the microarray were selected for the quantitative analysis. The microarray study was conducted in an ecotoxicological context: the integration of gene expression with organism and population level endpoints (survival, growth, reproduction) was investigated, to test the ecotoxicological relevance of AgNPs-induced gene expression. Results provide insight into the global transcription response of C.elegans to AgNPs exposure and also contribute to enhance the potential of C.elegans microarray in ecotoxicology (ecotoxicogenomics). key word: ecotoxicogenomics Experiment Overall Design: Young adults of wildtype C.elegans from age-synchronized population were exposed to 0.1mg/L of AgNPs for 24 h and RNA extraction and hybridization were subsequently conducted using C.elegans Genome array (Affymetrix).

2009-03-07 | E-GEOD-14932 | biostudies-arrayexpress

Transcription profiling of C. elegans exposed to BPA, DEHP and NP - ecotoxicogenomic analysis

Project description:Gene expression analysis was conducted on the wildtype Caenorhabditis elegans exposed to bisphenol A (BPA), di(2-ethylhexyl) phthalate (DEHP) and nonylphenol (NP) using whole genome microarray. The microarray study was conducted in an ecotoxicological context, by investigating the response of global gene expression with that of classical toxicological endpoints, such as, mortality, growth, reproduction and development. Results provide insight into global transcription response of C.elegans to these endocrine disrupting chemicals exposure and also contribute to enhance the potential of C.elegans microarray in ecotoxicology (ecotoxicogenomics). key word : ecotoxicogenomics Experiment Overall Design: Young adults of wildtype C.elegans from age-synchronized population were exposed to NP, DEHP and BPA at the concentrations equivalent to 1/100 of 24h LC50 of each chemical, for 24 h and RNA extraction and hybridization were subsequently conducted using C.elegans Genome array (Affymetrix).

2009-03-07 | E-GEOD-15016 | biostudies-arrayexpress

mRNA microarray analysis on young adults C.elegans exposed to GO and rGO

Project description:In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to GO and rGO on nematode, Caenorhabditis elegans. We performed whole genome DNA microarray experiments using age synchronized young adult C. elegans population exposed to GO and rGO for 24h. We used whole genome microarrays to screen for global changed in C. elegans transcription profiles and with subsequent quantitative analysis conducted on selected genes. Young adults of C.elegans were selected for RNA extraction and hybridization on Affymetrix microarrays.

2016-07-19 | E-GEOD-84489 | biostudies-arrayexpress

mRNA microarray analysis on young adults C.elegans exposed to UV, TiO2 and UV+TiO2

Project description:In order to evaluate the identification of genes and pathways, the global gene expression profiles were assessed in response to UV, TiO2 and UV+TiO2 on nematode, Caenorhabditis elegans. We performed whole genome DNA microarray experiments using age synchronized young adult C. elegans population exposed to UV, TiO2 and UV+TiO2 for 24h. We used whole genome microarrays to screen for global changed in C. elegans transcription profiles and with subsequent quantitative analysis conducted on selected genes. Young adults C. elegans were selected for RNA extraction and hybridization on Affymetrix microarrays.

2016-07-16 | E-GEOD-84441 | biostudies-arrayexpress

Differential modification of the C. elegans proteome in response to acute and chronic gamma radiation: link with reproduction decline

Project description:Ecosystems are chronically exposed to ionizing radiations. But environmental risk assessment of chronic exposure suffers from a lack of knowledge. Extrapolation of data from acute to chronic exposure is not always relevant, and can lead to uncertainties. In fact, effects could be different between the two irradiation modes, especially regarding reproduction endpoint, which is an ecologically relevant parameter . The free living nematode Caenorhabditis elegans is a particularly appropriate model organism to address this proteomic issues. With its fully sequenced genome and its short life cycle, C. elegans has been successfully used to study acute and chronic irradiation effects and their consequences on germline development and hatching. Results showed that a decrease of the number of progeny associated with a decrease of hatching success occurred from and above 30 Gy of acute irradiation.. In the present study, we decided to refine the understanding of molecular mechanisms of acute and chronic irradiation by a global proteome analysis. To do so, C. elegans were exposed to 3 common cumulated doses between acute and chronic exposure. These 3 doses, lower than the doses for which an effect on the reproduction was shown, were susceptible to allow us to find early and sensitive biomarkers of a reproduction decline. After exposure, global modification of the proteome expression was studied using a label free LC-MS/MS proteomic approach. Our objectives were to test the following hypotheses: (1) whether or not proteome expression varied with the dose, and with the irradiation mode; (2) if proteome expression modification was associated with effects on reproduction, with potential direct implications for ecological risk assessment.

2020-10-15 | PXD011731 | Pride

Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics

Project description:We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval stages (L1 to L4), dauer and L1/L4 post dauer. Histones were analyzed by our optimized middle-down protein sequencing platform using high mass accuracy tandem mass spectrometry. This allows quantification of intact histone tails and detailed characterization of distinct histone tails carrying co-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during development and it was mutually exclusive of the active marks H3K18ac, R26me1 and R40me1, suggesting a role for H3K23me3 in to silent chromatin. We observed distinct PTM profiles for normal L1 larvae and for L1-post dauer larvae, or L4 and L4 post-dauer, suggesting that histone PTMs mediate an epigenetic memory that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms.

2015-11-02 | PXD002525 | Pride

Alterations in gene expression in Caenorhabditis elegans associated with exposure to several classes of toxic industrial chemicals/materials.

Project description:Effective toxicological testing of the vast number of new and existing chemicals currently in use will require efficient and cost effective methods. We evaluated the utility of a simple, low cost toxicity testing system employing the nematode Caenorhabditis elegans to identify toxicologically relevant changes in gene expression. The objective of this research is to determine genomic and proteomic responses in the model nematode C. elegans to exposures to representatives of several classes of toxic industrial chemicals/materials (TICs/TIMs). A total of 3 chemicals (acrylamide, cadmium chloride, and mercuric chloride) were used in these experiments. Affymetrix GeneChip for C. elegans was used to examine genome-wide responses in the 19,000+ genes of this model organism. Mid-vulval L4 worms were exposed to one of four concentrations of acrylamide, cadmium or mercury for 4h and 8h. Exposures were performed in triplicate.

2012-11-28 | E-GEOD-42592 | biostudies-arrayexpress

Function, targets and evolution of Caenorhabditis elegans piRNAs (small RNA-Seq)

Project description:piRNAs are required to maintain germline integrity and fertility but their mechanism of action is poorly understood. Here we demonstrate that C. elegans piRNAs silence transcripts in trans through imperfectly complementary sites. We find that target silencing is independent of Piwi endonuclease activity or “slicing”. Instead, we show that piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene, pseudogene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes but not pseudogenes or transposons. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNAi in C. elegans. 7 small RNA libraries were sequenced as part of 25 flow cell lanes on the Illumina GA II platform. Samples were treated with tobacco acid pyrophosphatase to allow cloning of small RNAs with a 5'-triphosphate. Samples were labelled for multiplexing using 4-bp 5'-barcodes or barcodes included in Illumina TruSeq adapters. In most cases a single flow cell lane included several multiplexed libraries.

2012-06-18 | E-GEOD-28617 | 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