Caenorhabditis elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA113821 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Wild-type and daf-16(mgDf50) L1 larvae 3 hours after hatching in the presence or absence of food
| PRJNA387550 | ENA
Project description:When C. elegans larvae hatch in the absence of food they persist in a stress resistant, developmentally arrested state (L1 arrest). We characterized mRNA expression genome-wide in a pair of bifurcating time series starting in the late embryo and proceeding through the hatch in the presence and absence of food (E. coli). We used Affymetrix C. elegans expression arrays to measure gene expression in 18 total timepoint/conditions in three biological replicates. Keywords: time course; plus/minus food
2009-02-27 | GSE11055 | GEO
Project description:Whole starved L1 larvae were collected at twelve time points spanning from hatching to death.
2022-10-11 | GSE173656 | GEO
Project description:Whole L1 larvae were collected from GC1459 [naSi2 [pGC550 (mex-5p::mCherry::H2B::nos-2 3'UTR +unc-119(+))] II; unc-119(ed3) III ?; daf-18(ok480) IV] and GC1171 [naSi2 [pGC550 (mex-5p::mCherry::H2B::nos-2 3'UTR +unc-119(+))] II; unc-119(ed3) III] strains up to two hours after hatching without food.
2021-06-21 | GSE151299 | GEO
Project description:Expression data from C. elegans in the presence or absence of copper sulfate
| PRJNA182900 | ENA
Project description:Expression data from Caenorhabditis elegans let-418(RNAi), mep-1(RNAi) and gfp(RNAi) L1 larvae. The C. elegans genome encodes two homologs of the human protein Mi-2, namely LET-418 and CHD-3. LET-418 plays an essential role during development; its depletion leads to a pleiotropic and lethal phenotype that includes larval arrest, an everted vulva and sterility. Without maternal contribution, let-418 mutants stop their development at the L1 larval stage (von Zelewsky et al., 2000). We further characterized this arrest and showed that it is very similar to the L1 diapause induced by starvation; both germline and somatic cells remain in a quiescent state in let-418 L1 arrested larvae, indicating that LET-418 activity is required to bypass the L1 arrest in presence of food. The let-418 L1 larvae express ectopically the P granule component PGL-1 in somatic cells (Unhavaithaya et al., 2002). Interestingly, the phenotype of mep-1 mutants is remarkably similar to that of let-418: RNAi targeting mep-1 also induced an L1 arrest phenotype; furthermore, MEP-1 and LET-418 have been shown to physically interact (Unhavaithaya et al., 2002 and M. Passannante). The null allele mep-1(q660) is temperature sensitive and shows a more severe phenotype at higher temperatures. At 20°C, about 10% of mep-1 homozygotes derived from heterozygous mothers arrest as young larvae, whereas the remaining 90% develop into sterile adults (Belfiore et al., 2002). Later in development, the somatic gonad is affected in mep-1(q660) mutants. This results in an abnormal and disorganized gonad, a phenotype also observed in let-418(s1617) mutants. Both let-418 and mep-1 mutants produce a very limited number of oocytes and have pseudovulvae derived from P8.p (Belfiore et al., 2002; von Zelewsky et al., 2000 and C. Wicky, personal communication). Preliminary quantitative real-time PCR revealed that the expression of genes coding for P granule components was deregulated in both mep-1(RNAi) and let-418(RNAi) L1 larvae (data not shown). To further investigate this issue, we performed a complete gene expression analysis. Given the fact that mep-1(q660) mutants are sterile, we used RNA interference to generate mep-1 depleted worms. Bacteria expressing gfp dsRNA (pPE128.110 in HT115) were used as reference, since RNA interference may induce gene expression changes by itself. C. elegans L1 larvae treated with RNA interference were selected for RNA extraction and hybridization on Affymetrix microarrays. Synchronized wild type L4 animals were grown at 25° on bacteria expressing either gfp, let-418 or mep-1 dsRNA. Eggs were collected by bleaching gravid adults and allowed to hatch in the absence of food at 25°C. Newly hatched L1 larvae were fed on bacteria expressing the different dsRNA for three hours to recover from starvation. Three replicates per RNAi.
2010-10-31 | E-GEOD-21376 | biostudies-arrayexpress
Project description:Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence and absence of arsenite
| PRJNA198476 | ENA
Project description:Ultraviolet C radiation (UVC) damages the nuclear and mitochondrial genomes; this damage is repaired in the nuclear but not mitochondrial genome. Ethidium bromide (EtBr) inhibits mitochondrial DNA replication. We were interested in the transcriptomic response to exposure to UVC, EtBr, and the combination. The UVC exposure protocol results in a high level of mitochondrial DNA damage, and a low level of nuclear DNA damage (because of repair). We exposed age-matched L1-stage Caenorhabditis elegans to ultraviolet C radiation (UVC ) three times, separated in time by 24 h, in the absence of food. After the third exposure, larvae were placed on K agar plates with OP50 bacterial food. In some cases ethidium bromide was also used. Nematodes were sampled for RNA isolation several times.
2012-10-01 | E-GEOD-38997 | biostudies-arrayexpress
Project description:Yilmaz2016 - Genome scale metabolic model -
Caenorhabditis elegans (iCEL1273)
This model is described in the article:
A Caenorhabditis elegans
Genome-Scale Metabolic Network Model.
Yilmaz LS, Walhout AJ.
Cell Syst 2016 May; 2(5): 297-311
Abstract:
Caenorhabditis elegans is a powerful model to study
metabolism and how it relates to nutrition, gene expression,
and life history traits. However, while numerous experimental
techniques that enable perturbation of its diet and gene
function are available, a high-quality metabolic network model
has been lacking. Here, we reconstruct an initial version of
the C. elegans metabolic network. This network model
contains 1,273 genes, 623 enzymes, and 1,985 metabolic
reactions and is referred to as iCEL1273. Using flux balance
analysis, we show that iCEL1273 is capable of representing the
conversion of bacterial biomass into C. elegans biomass
during growth and enables the predictions of gene essentiality
and other phenotypes. In addition, we demonstrate that gene
expression data can be integrated with the model by comparing
metabolic rewiring in dauer animals versus growing larvae.
iCEL1273 is available at a dedicated website
(wormflux.umassmed.edu) and will enable the unraveling of the
mechanisms by which different macro- and micronutrients
contribute to the animal's physiology.
This model is hosted on
BioModels Database
and identified by:
MODEL1604210000.
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To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
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Public Domain Dedication for more information.
2016-11-03 | MODEL1604210000 | BioModels
Project description:When C. elegans larvae hatch in the absence of food they persist in a stress resistant, developmentally arrested state (L1 arrest). We characterized mRNA expression genome-wide in a pair of bifurcating time series starting in the late embryo and proceeding through the hatch in the presence and absence of food (E. coli). We used Affymetrix C. elegans expression arrays to measure gene expression in 18 total timepoint/conditions in three biological replicates. Experiment Overall Design: Nematode populations were staged such that they hatched withing a 2.5 hr window, and time point zero (0 hr) corresponds to when 50% of the population had hatched. RNA was isolated with TRIzol and 100 ng was used for T7 RNA polymerase-based mRNA amplification and biotin labeling using MessageAmp II-Biotin Enhanced kit (Ambion). Labeled cRNA was fragmented, hybridized to the Affymetriz array, and scanned according to the manufacturerâs protocol.
2009-03-07 | E-GEOD-11055 | biostudies-arrayexpress