Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray on an infection time-series of Orsay virus in three Caenorhabditis elegans genotypes

ABSTRACT: This experiment investigates the temporal dynamics in gene expression upon Orsay virus infection in the nematode Ceanorhabditis elegans. Three different strains were infected: JU1580, N2, and CB4856. Of these, JU1580 is highly susceptible, N2 moderately susceptible, and CB4856 the most resistant strain. The goal of the experiment was to identify genes that show different expression dynamics over the time-course of the infection. We (mock-)infected 40h-old C. elegans populations with Orsay virus and took samples over a 32-hour spanning time-course. For each treatment-strain combination 12 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene-expression dynamics of previously identified genes (e.g. from literature and from a highly replicated N2 versus CB4856 experiment) were analyzed.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Mark Sterken

PROVIDER: E-MTAB-7573 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Microarray on Caenorhabditis elegans N2 and CB4856 infected with Orsay virus

Project description:This experiment investigates the gene expression differences upon Orsay virus infection in the Caenorhabdits elegans strains N2 and CB4856. Assays measuring viral load found that the N2 strain displays higher viral loads upon infection than the CB4856 strain. The goal of the experiment was to identify gene-expression differences that could explain the differences in viral load. We (mock-)infected 26h-old C. elegans populations with Orsay virus and took samples after 30h of infection. For each treatment-strain combination 8 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray.

2020-07-08 | E-MTAB-7574 | biostudies-arrayexpress

Microarray on mock-treated or Orsay virus infected males and hermaphrodites of Caenorhabditis elegans

Project description:This experiment investigates changes in gene expression upon Orsay virus infection and between males and hermaphrodites in the nematode Ceanorhabditis elegans. The laboratory reference strain N2 was used. For this strain, males are less susceptible to Orsay virus infection than hermaphrodites. The goal of the experiment was to identify genes that show different expression patterns for both sexes upon Orsay virus infection. We mock-treated or infected 48h-old C. elegans populations with Orsay virus and took samples 30-hours after infection. For each treatment-sex combination 8 samples were collected. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene-expression dynamics of previously identified genes (e.g. from literature and from a highly replicated N2 versus CB4856 experiment) were analyzed.

2020-09-13 | E-MTAB-9561 | biostudies-arrayexpress

Gene expression effects in Caenorhabditis elegans strains of feeding on Erwinia rhapontici or Escherichia coli

Project description:Diet can have a strong impact on development, to test this effect the strains N2, CB4856, three strains from Orsay (JU1581, JU1944, and JU1949), and three strains from Santeuil (JU1921, JU1930, and JU1932) were grown on two different food-sources. These sources were the standard lab food, Escherichia coli OP50, and the Gram-negative plant pathogen Erwinia rhapontici. The effect of these bacteria on development could also be measured by the start of reproduction, which was delayed while feeding on E. coli. To measure the transcriptional effects, age-synchronized strains were grown for 48 hours at 20 degrees Celsius. The impact of food-source on gene expression was determined by a transcriptional ruler based on the strain N2 (E-MTAB-7019).

2019-07-12 | E-MTAB-8129 | biostudies-arrayexpress

Dynamic gene expression of two Caenorhabditis elegans wild type strains (N2 and CB4856)

Project description:We analyzed the consequences of recombination in gene expression. For this, we measured expression patterns in two C. elegans wild types, N2 and CB4856 (CB). We compare these profiles with gene expression values from a Recombinant Inbred Population (RIL) derived from the same wild types. Expression values of the RILs (GSE17071) were obtained from ViÃ±uela et al. (Genome Research, 2010). N2 and CB strain nematodes were cultured in identical conditions. Likewise, mRNA was extracted at three different ages (juveniles, reproductive and old worms) to investigate the transcriptional consequences of recombination in aging worms. Then, we explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in natural isolates. Moreover, we investigated the progression of those parameters with age. In total, 14 dual-color microarrays were done on two wild type strains (N2 and CB4856) and three age groups (40, 96, and 214 hours). 5 replicates of t1 (juvenile) and t3 (senescent) samples, and 4 replicates of t2 (reproductive) samples, in a dye-swap design.

2012-03-31 | E-GEOD-22887 | biostudies-arrayexpress

Microarray of C. elegans wild types N2 and CB4856 after Orsay virus infection and heat-shock treatment.

Project description:This explorative study investigated the transcriptional response of C. elegans wild types N2 and CB4856 after Orsay virus infection and Heat shock (n=1). Each strain had a sample that was heat-shocked and infected, one that was heat-shocked and mock-infected, one that was only infected and one that only underwent a mock infection. Age synchronized worms were treated separately according to different treatments mentioned before. After flash freezing, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.

2021-03-08 | E-MTAB-10214 | biostudies-arrayexpress

Gene expression of 47 Caenorhabditis elegans strains from Orsay and Santeuil

Project description:This study investigated the role of local genetic variation on gene expression. To this end, gene expression variation between strains isolated from two locations (Orsay and Santeuil) was investigated by microarray. As an outgroup the N2, CB4856, WN2001, WN2002, WN2003, JU314 and JU396 were used. Age-synchronized strains were grown for 47 hours at 20 degrees Celsius, where after strains were sampled and RNA was isolated. Labelled cRNA was hybridized to microarray to assess the impact of local genetic variation on gene expression. DNA hybridization complementing this study can be found in E-MTAB-8126.

2019-07-12 | E-MTAB-8132 | biostudies-arrayexpress

Small RNA seq on C. elegans males and hermaphrodites that were either mock treated or exposed to the OrV

Project description:In this experiment we exposed L4 males and hermaphrodites to mock (M9) or Orsay virus for one hour in liquid. Subsequently, nematodes were collected 30 hours after exposure. The small RNAs were isolated and sequenced.

2021-07-01 | E-MTAB-10642 | biostudies-arrayexpress

DNA hybridization of 48 Caenorhabditis elegans strains from Orsay and Santeuil

Project description:Genetic variation between strains isolated from two locations (Orsay and Santeuil) was investigated by differential hybridization to microarrays. As an outgroup the N2, CB4856, WN2001, WN2002, WN2003, JU314 and JU396 were used. DNA was isolated from isogenic populations.

2019-07-12 | E-MTAB-8126 | biostudies-arrayexpress

Comparison of gene expression profiles between N2 wild-type C. elegans and an nhr-8(hd117) mutant

Project description:Transcriptional profiling of N2 vs. nhr-8 mutant worms, aiming to identify direct and indirect targets of the nuclear receptor. Seven independent synchronized populations of N2 and nhr-8(hd117) animals were grown from eggs on low cholesterol plates at 25 degrees C until mid-L3 larval stage and collected for microarray RNA expression analysis.

2013-08-06 | E-GEOD-48675 | biostudies-arrayexpress

Natural genetic variation on proteome level in Caenorhabditis elegans

Project description:Natural genetic variation is the raw material of evolution and influences disease development and progression. To analyze the effect of the genetic background on protein expression in the nematode C. elegans (Caenorhabditis elegans), the two genetically highly divergent wild-type strains N2 (Bristol) and CB4856 (Hawaii) were compared quantitatively. In total, we quantified 3,238 unique proteins in three independent SILAC (stable isotope labeling by amino acids in cell culture) experiments. The differentially expressed proteins were enriched for genes that function in insulin-signaling and stress response pathways.

2016-03-11 | PXD002010 | 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