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Gene expression of 47 Caenorhabditis elegans strains from Orsay and Santeuil

ABSTRACT: 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.

INSTRUMENT(S): High resolution C. scanner

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Mark Sterken

PROVIDER: E-MTAB-8132 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene-environment and protein-degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis elegans populations.

Volkers Rita J M RJ Snoek L Basten LB Hubar Caspara J van Hellenberg CJ Coopman Renata R Chen Wei W Yang Wentao W Sterken Mark G MG Schulenburg Hinrich H Braeckman Bart P BP Kammenga Jan E JE

BMC biology 20130819

<h4>Background</h4>Analyzing and understanding the relationship between genotypes and phenotypes is at the heart of genetics. Research on the nematode Caenorhabditis elegans has been instrumental for unraveling genotype-phenotype relations, and has important implications for understanding the biology of mammals, but almost all studies, including forward and reverse genetic screens, are limited by investigations in only one canonical genotype. This hampers the detection and functional analysis of ...[more]

PMID: 23957880

Similar Datasets

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

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

Transcriptome profiling by microarray of Caenorhabditis elegans MT2124 x CB4856 RILs used for eQTL mapping

Project description:We crossed the MT2124 strain carrying the let-60 (n1046) gain of function mutation with the wild-type strain CB4856. From this cross a panel of mutation introgression recombinant inbred lines (miRILs) was generated. Using this population, the influence of genetic variation on the the let-60 (gf) mutation can be investigated. This analysis can pinpoint genetic loci A panel of 33 miRILs, the parental strains (4x), and transgenic lines amx-2(lf);Si[amx-2(Bristol)];let-60(gf) and amx-2(lf);Si[amx-2(Hawaii)];let-60(gf) containing the N2- or CB4856-allele of amx-2 in a amx-2(lf);let-60(gf) background were sampled. All the strains were grown on nematode growth medium dishes seeded with E. coli OP50. The temperature at which the strains were kept was 20 degrees Celsius and the strains were grown for 72 hours after synchronization by bleaching. Thereafter RNA was isolated, labelled, and hybridized on microarray. The gene expression profiles of the miRILs were used for eQTL mapping. The gene expression profiles of the transgenic strains were used for trans-band confirmation.

2017-07-21 | E-MTAB-5856 | 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

Gene expression profiling in control, heat-shock, and recovery treatment in an introgression line population of Caenorhabditis elegans L4 larvae

Project description:This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in an N2xCB4856 introgression line population of Caenorhabditis elegans. The goal is to compare the effect of small CB4856 introgressions in an N2 genetic background versus a previously conducted experiment using recombinant inbred lines (RILs) derived from the same parental strains. We exposed ILs to a control (56 ILs), heat-stress (56 ILs), and recovery treatment (55 ILs). Additionally, also both parental strains, N2 and CB4856 were exposed to these three treatments (in at least 3 replicas per treatment). More specifically, these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for comparison versus findings in the RIL population (E-MTAB-5779).

2019-05-29 | E-MTAB-7424 | biostudies-arrayexpress

Gene expression profiling in control, heat-shock, and recovery treatment in a RIL population of Caenorhabditis elegans L4 larvae

Project description:This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in a N2xCB4856 RIL population of Caenorhabditis elegans. The goal is to identify genetic variation linked to differences in gene expression. We exposed 48 RILs per treatment to a control, heat-stress, and recovery treatment. More specifically these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for eQTL mapping.

2017-05-30 | E-MTAB-5779 | biostudies-arrayexpress

Microarray analysis of Caenorhabditis elegans exposed to six distinct water samples

Project description:In this study, we exposed Caenorhabditis elegans wild types N2 to water collected from six sources in the Dutch village Sneek. The sources were: wastewater from a hospital, a community (80 households), a nursing home, influent into the local municipal wastewater treatment plant, effluent of the wastewater treatment plant, and surface water samples. The goal of the experiment was to determine if C. elegans can be used to identify pollutants in the water by transcriptional profiling. Age synchronized worms at developmental L4 larval stage were exposed to treatment for 24 hours. After flash freezing the samples, RNA was isolated, labeled and hybridized on oligo microarray (Agilent) slides.

2022-12-03 | E-MTAB-11260 | biostudies-arrayexpress

Comparative genomic hybridization of rat SJL sub-strains of an experimental autoimmune encephalomyelitis (EAE) rodent model of Multiple Sclerosis (MS)

Project description:Copy number variation in two SJL sub-strains of an experimental autoimmune encephalomyelitis (EAE) rodent model of Multiple Sclerosis (MS)

2010-02-26 | E-MEXP-2534 | 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

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