Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

85 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Lisa van Sluijs

PROVIDER: E-MTAB-9561 | 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 an infection time-series of Orsay virus in three Caenorhabditis elegans genotypes

Project description: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.

2020-07-14 | E-MTAB-7573 | 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

Analysis of small RNA response to viral infection in C.elegans

Project description:Dissection of the small RNA pathway required for generation of an antiviral small RNA response Small non-coding RNA (~15-30nt) was extracted from animals infected with the Orsay virus

2013-06-01 | E-GEOD-41693 | biostudies-arrayexpress

RNA-seq of whole body L2 females, L2 hermaphrodites, L2 converted females (hermaphrodite-fated larvae induced to develop as females), adult males and mixed stages individuals from the three-sexed nematode Auanema rhodensis

Project description:The nematode Auanema rhodensis is trioecious (co-occurrence of males, females and self-fertile hermaphrodites). To better understand its sex determination system, we have compared the transcriptomic profiles of early (L2) females, hermaphrodites and converted females (hermaphrodite-fated larvae induced to develop as females). Additionally, we sequenced the transcriptome of adult males and individuals from various stages and sexes (mixed stages samples) to compare global gene expression profiles along the assembled draft chromosomes of A. rhodensis (BioProject PRJEB29492). The RNA-seq data was also used to predict genes in the assembled genome. We generated three biological replicates for each RNA-seq condition (L2 females, L2 converted females, L2 hermaphrodites, males and mixed stages). Comparisons of the expression profiles of the L2 conditions was performed to identify genes potentially involved in the sexual differentiation process, using a standard RNA-seq comparison approach. Briefly, the cleaned reads were aligned to the genome using STAR, the abundance and identification of differentially expressed genes were assessed using FeatureCounts and DEseq2 (using as thresholds an absolute log2(Fold Change) >= 2 and an FDR <0.01).

2019-02-11 | E-MTAB-7667 | 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

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

Paternal RNA contributions in the C. elegans zygote

Project description:Development of the early embryo is thought to be mainly driven by maternal gene products and post-transcriptional gene regulation. Here, we used metabolic labeling to show that RNA can be transferred by sperm into the embryo. To identify genes with paternal expression in the embryo, we performed crosses of males and females from divergent C. elegans strains. RNA sequencing of mRNAs and small RNAs in the 1-cell hybrid embryo revealed that about two hundred paternal mRNAs are reproducibly expressed in the embryo, and that about half of assayed endogenous siRNAs and piRNAs are also of paternal origin. Together, our results suggest an unexplored paternal contribution to early development. To reveal the identity of paternal RNA molecules, we performed a cross of males and females from two divergent C. elegans strains because we reasoned that sequencing of embryonic RNA and SNP analysis should then identify and quantify maternal and paternal transcripts. These sequencing experiments were carried out in purified hybrid 1-cell embryos and comprised small RNAs and mRNAs. For comparison we sequenced mRNAs and small RNAs from the parental strains: paternal (Hawaiian males, CB4856) and maternal (fem-1(hc17ts)/TX189(OMA-1::GFP). For the annotation of strain specific mutations (SNPs) we sequenced mRNA and small RNAs extracted from whole worms. All experiments were performed in at least two independent biological replicates.

2014-06-04 | E-GEOD-57351 | 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

Global genetic robustness of the alternative splicing machinery in C. elegans

Project description:Alternative splicing is considered a major mechanism for creating multicellular diversity from a limited repertoire of genes. Different isoforms can be produced at the same time in the same cell type and their ratios can be the same or different between divergent genotypes. Here, we studied genetic variation in alternative splicing patterns in a large recombinant inbred population of C. elegans, using whole-genome tiling arrays. This experiment allowed us to detect heritable differences in gene expression with exquisite sensitivity and resolution, and we detected 435 genes with substantial heritable variation for at least one exon. Nonetheless, we find only a very small number of examples of heritable variation in alternative splicing (22 transcripts), and most of these genes co-localize with the associated genomic loci. This is in striking contrast to earlier observations in humans, which showed much less genetic robustness. C. elegans recombinant inbred lines were generated and genotyped as described in (Li et al. 2006). mRNA was isolated from 60 RILs reared under standard condition and hybridized to Affymetrix 1.0 C. elegans tiling arrays. The hybridization was done by ServiceXS (Leiden, The Netherlands).

2011-01-01 | E-GEOD-15778 | biostudies-arrayexpress

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