Ontology highlight
ABSTRACT:
PROVIDER: PRJNA481583 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7533650_1.fastq.gz | Fastqsanger.gz | |||
| SRR7533650_2.fastq.gz | Fastqsanger.gz | |||
| SRR7533670_1.fastq.gz | Fastqsanger.gz | |||
| SRR7533670_2.fastq.gz | Fastqsanger.gz | |||
| SRR7533680_1.fastq.gz | Fastqsanger.gz |
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Project description:Mutation generates the heritable variation that genetic drift and natural selection shape. In classical quantitative genetic models, drift is a function of the effective population size and acts uniformly across traits, while mutation and selection act trait-specifically. We identified thousands of quantitative trait loci (QTL) influencing transcript abundance traits in a cross of two C. elegans strains; although trait-specific mutation and selection explained some of the observed pattern of QTL distribution, the pattern was better explained by trait-independent variation in the intensity of selection on linked sites. Our results suggest that traits in C. elegans exhibit different levels of variation less because of their own attributes than because of differences in the effective population sizes of the genomic regions harboring their underlying loci.
2010-10-01 | GSE23857 | GEO
Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers. Twelve C. elegans natural isolate samples were studied. There were no replicates or dye-swap hybridizations.
2010-05-17 | E-GEOD-19440 | biostudies-arrayexpress
Project description:Background: Copy number variation is an important component of genetic variation in higher eukaryotes. The extent of natural copy number variation in C. elegans is unknown outside of 2 highly divergent wild isolates and the canonical N2 Bristol strain. Results: We have used array comparative genomic hybridization (aCGH) to detect copy number variation in the genomes of 12 natural isolates of Caenorhabditis elegans. Deletions relative to the canonical N2 strain are more common in these isolates than duplications, and indels are enriched in multigene families on the autosome arms. Among the strains in our study, the Hawaiian and Madeiran strains (CB4856 and JU258) carry the largest number of deletions, followed by the Vancouver strain (KR314). Overall we detected 510 different deletions affecting 1136 genes, or over 5% of the genes in the canonical N2 genome. The indels we identified had a median length of 2.7 kb. Since many deletions are found in multiple isolates, deletion loci were used as markers to derive an unrooted tree to estimate genetic relatedness among the strains. Conclusion: Copy number variation is extensive in C. elegans, affecting over 5% of the genes in the genome. The deletions we have detected in natural isolates of C. elegans contribute significantly to the number of deletion alleles available to researchers. The relationships between strains are complex and different regions of the genome possess different genealogies due to recombination throughout the natural history of the species, which may not be apparent in studies utilizing smaller numbers of genetic markers.
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Project description:Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans. We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA levels with a heritability ranging from 32-82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite QTL (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs) we were able to narrow down both mQTL to a 1.4 Mbp and a 3.6 Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81. Overall, this systems approach provides us with a powerful platform to study the genetic basis of C. elegans metabolism. Furthermore, it allows us to investigate interventions, such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.
2018-07-05 | ST000999 | MetabolomicsWorkbench
Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid and jasmonic acid, have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs) affecting host resistance responses. In order to identify an appropriate RIL population to map QTL controlling disease resistance responses, we performed a parental survey of 7 different Arabidopsis accessions. We treated vegetatively grown plants with either salicylic acid or a control solution, and harvested the plants at 3 different time points after chemical treatment. We present Affymetrix GeneChip microarray expression data for 3 biological replications of this parental survey
2005-10-26 | E-TABM-51 | biostudies-arrayexpress
Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, eQTLs) affecting host resistance responses. We surveyed recombinant inbred lines (RILs) from a population derived from a cross of inbred Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) in order to map eQTLs controlling ELPs. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 28 hours after chemical treatment. Here we present Affymetrix GeneChip microarray expression data for 8 biological replications of the control (Silwet) samples for Bay-0 and Sha.
2007-03-01 | E-TABM-224 | biostudies-arrayexpress
Project description:Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains Bristol N2 and Hawaii CB4856 to enable quantitative trait loci (QTL) mapping. Variation in gene expression was greater in the RILs than in the parental lines, at the proteome as well as at the transcriptome levels. We detected a trans-QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels.
2016-02-16 | GSE77905 | GEO
Project description:Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains Bristol N2 and Hawaii CB4856 to enable quantitative trait loci (QTL) mapping. Variation in gene expression was greater in the RILs than in the parental lines, at the proteome as well as at the transcriptome levels. We detected a trans-QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels. Parental genotypes N2 (3x) and CB4856 (3x) and 47 RILs from (Li etal 2006; Vinuela etal 2010 and Elvin etal 2011)
2016-02-16 | E-GEOD-77905 | biostudies-arrayexpress
Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We assessed Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) for natural variation in the response to JA. We treated vegetatively grown plants with either JA or a control solution (Silwet), and harvested the plants 4, 28, or 52 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for Bay-0 and Sha. These GeneChips were used to generate genetic markers which allowed the development of high-density haplotype maps of a Bay-0 x Sha RIL population.
2006-11-14 | E-TABM-60 | biostudies-arrayexpress
Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We assessed Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) for natural variation in the response to SA. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 4, 28, or 52 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for Bay-0 and Sha. These GeneChips were used to generate genetic markers which allowed the development of high-density haplotype maps of a Bay-0 x Sha RIL population.
2007-01-01 | E-TABM-61 | biostudies-arrayexpress