Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A genomic signature of gene-environment interactions in C. elegans

ABSTRACT: The phenotype is an interplay between genetic and environmental components, however the relationship between these two is difficult to predict. For any particular environment only a handful of genes show gene environment interaction [refs]. This may imply that certain constrains prevent genes to participate in gene environment interaction that possibly could be used to predict potential targets for such interaction under different sets of environmental conditions. Our approach was to culture 6 C. elegans strains (5 geographical isolates + 1 mutant straint) at 20Â°C, then split the culture into 5 conditions. We measured mRNA abundances in 4-cell stage embryos using microarray with three separately collected 50-embryo replicates collected for each combination of strain and environment. 90 microarrays of C. elegans for 6 strains * 5 conditions in triplicates.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Itai Yanai

PROVIDER: E-GEOD-34650 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Heat stress reveals heritable changes in mRNA profile in 4-cell stage embryos of the nematode Caenorhabditis elegans.

Project description:For centuries, scientists have wondered whether the responses of animals and plants to environmental change can be transmitted to subsequent generations. Lately, there been much interest in the inheritance of information that is not encoded by differences in DNA sequence. Here we show that transient, mild heat stress results in a heritable change in the messenger RNA profile of early-stage C. elegans embryos. After heat stress is removed for one generation, abundances of most, but not all, mRNAs have relaxed to the unstressed state. Our approach was to culture worms at 20°C, then split the culture into 20°C control and 25°C treatment, followed by return of the 25°C culture to 20°C. Specifically, we compared mRNA abundances in 4-cell stage embryos collected from mothers kept at 20°C, with embryos whose mothers were also reared at 20°C but whose grandparents had been reared at 25°C. Two strains and two generations under a treatment and under a control condition were analyzed by microarray with three separately collected 50-embryo replicates for each combination, for a total of 24 samples.

2011-12-31 | E-GEOD-30666 | biostudies-arrayexpress

C. briggsae developmental timecourse

Project description:To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays. We designed two organism-specific microarrays which were then manufactured by Agilent as 44k arrays. Probes were designed to target the coding region, preferentially near the 3â end, as well as in the presumptive 3â UTR, up to 150bp downstream of the stop codon. 50-60mer probes were determined using OligoWiz (Wernersson and Nielsen 2005) which selects oligos based upon their cross-hybridization to other coding sequences, Tm, position along the transcript, folding potential, and low-complexity in the sequence. The probes were also restricted against spanning splice junctions to avoid missing transcripts due to errors in gene structure predictions. Each gene was assigned between one and five probes, where the probe with the best overall score was selected as the âA-probeâ, and the remaining ranked âBâ through âEâ.

2010-05-06 | E-GEOD-15233 | biostudies-arrayexpress

C. elegans developmental timecourse

Project description:To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays. We designed two organism-specific microarrays which were then manufactured by Agilent as 44k arrays. Probes were designed to target the coding region, preferentially near the 3’ end, as well as in the presumptive 3’ UTR, up to 150bp downstream of the stop codon. 50-60mer probes were determined using OligoWiz (Wernersson and Nielsen 2005) which selects oligos based upon their cross-hybridization to other coding sequences, Tm, position along the transcript, folding potential, and low-complexity in the sequence. The probes were also restricted against spanning splice junctions to avoid missing transcripts due to errors in gene structure predictions. Each gene was assigned between one and five probes, where the probe with the best overall score was selected as the ‘A-probe’, and the remaining ranked ‘B’ through ‘E’.

2009-08-31 | E-GEOD-15234 | biostudies-arrayexpress

C. briggsae and C. elegans developmental timecourses

Project description:This SuperSeries is composed of the following subset Series: GSE15233: C. briggsae developmental timecourse GSE15234: C. elegans developmental timecourse Refer to individual Series

2009-08-31 | E-GEOD-15551 | biostudies-arrayexpress

Global proteomics analysis reveals a role for histone variant H3.3 in the response to starvation

Project description:Periodic starvation of animals induces large shifts in metabolism, but may also influence many other cellular systems and can lead to adaption to prolonged starvation conditions. To date, there is limited understanding of how starvation affects gene expression, particularly at the protein level. Here, we have used mass spectrometry‐based quantitative proteomics to identify global changes in the C. elegans proteome due to acute starvation of young adult animals. Measuring changes in abundance of up to 7,000 proteins, we show that acute starvation rapidly alters the levels of hundreds of proteins, many involved in central metabolic pathways, highlighting key regulatory responses. Surprisingly, we also detect changes in the abundance of chromatin‐associated proteins including specific linker histones, histone variants and histone post‐translational modifications associated with the epigenetic control of gene expression. A null mutant for one of these proteins, the histone H3.3 variant HIS‐71, identified a subset of proteins whose abundance no longer varied in response to starvation. This mutant also displayed defects in starvation stress resistance and showed a reduced adult lifespan. To maximise community access to these data, they are presented in an online searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).

2015-06-17 | PXD001723 | Pride

Histone Demethylase UTX-1 Regulates the Caenorhabditis elegans Lifespan by Targeting the Insulin/IGF-1 Signaling Pathway

Project description:Epigenetic modifications are thought to be important for gene expression changes during development and aging. However, besides the Sir2 histone deacetylase in somatic tissues and H3K4 trimethylation in germlines, there is scant evidence implicating epigenetic regulations in aging. The insulin/IGF-1 signaling (IIS) pathway is a major lifespan regulatory pathway. Here we show that progressive increases in gene expression and loss of H3K27me3 on IIS components are due, at least in part, to increased activity of the H3K27 demethylase UTX-1 during aging. RNAi of the utx-1 gene extended the mean lifespan of C. elegans by ~30%, dependent on DAF-16 activity and not additive in daf-2 mutants. The loss of utx-1 increased H3K27me3 on the Igf1r/daf-2 gene and decreased IIS activity leading to a more "naive" epigenetic state. Like stem cell reprogramming, our results suggest that reestablishing epigenetic marks lost during aging might help "reset" the developmental age of animal cells. Examination of H3K27me3 in young and old worms without or with Utx-1 RNAi.

2011-11-22 | E-GEOD-29896 | biostudies-arrayexpress

Identification of tissue-specific SPD-5 and PLK-1 proximity interactors by direct and indirect TurboID

Project description:In this set of proof of principle experiments we compare the proximity interactomes obtained for two C. elegans centrosomal proteins, SPD-5 and PLK-1, by direct TurboID and indirect, GFP nanobody-targeted, TurboID in a range of different tissues, embryos, germ cell precursors and ciliated neurons.

2022-04-01 | PXD031970 | Pride

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

Project description:Physiologically based modelling using DEBtox (dynamic energy budget in toxicology) and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to atrazine (AZ). For AZ, the physiological mode of action predicted by DEBtox was increased cost for maintenance. The transcriptional analysis demonstrated that this increase resulted from effects on DNA integrity as indicated by changes in the expression of genes chromosomal repair. Our results have established that outputs from process based models and transcriptomics analyses can help to link mechanisms of action of toxic chemicals with resulting demographic effects. Such complimentary analyses can assist in the categorisation of chemicals for risk assessment purposes. Adults of C. elegans strain GE-31 exposed as biological replicate groups (approx 10,000) to a control and 4 concentrations of atrazine from L1 stage. Replicate populations were sampled 12 hours after the on-set of egg laying and hybridised against a common reference for purposes of normalisation. All experiments were conducted following a reference design with the reference sample compiled from a mixture of RNA extracted from control and cadmium-, fluoranthene-, atrazine- and copper-exposed worms from L1, L4 and adult life-stages. Use of this reference was intended to provide optimal coverage of the spotted genes.

2010-03-23 | E-GEOD-21008 | biostudies-arrayexpress

Bulk RNAseq on hemocytes from stage 16 embryos and wandering 3rd instar larvae of Drosophila melanogaster

Project description:The aim of this experiment is to compare the transcriptome of Drosophila hemocytes at two developmental stages: in stage 16 embryo, mostly free from any immune challenge and in larvae, which grow in bacteria rich environment. Transgenes inducing the expression of RFP in the hemocytes were used to sort the hemocytes from the two stages before carrying out the sequencing.

2020-03-12 | E-MTAB-8702 | biostudies-arrayexpress

DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in C. elegans

Project description:Assembly of the DNA helicase known as CMG (CDC45-MCM-GINS) is the key regulated step during DNA replication initiation in eukaryotes. Using the Caenorhabditis elegans embryo as a model system, we identify a new CMG assembly factor called DNSN-1, which associates with the BRCT-domain protein MUS-101. We show that DNSN-1 is required to recruit the GINS complex to chromatin and find that DNSN-1 positions GINS on the MCM-2-7 helicase motor, by direct binding of DNSN-1 to GINS and MCM-3, on interfaces that are important for initiation and essential for viability.

2023-10-24 | PXD044240 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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