Ontology highlight
ABSTRACT:
PROVIDER: PRJNA767876 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16154000_1.fastq.gz | Fastqsanger.gz | |||
| SRR16154000_2.fastq.gz | Fastqsanger.gz | |||
| SRR16154100_1.fastq.gz | Fastqsanger.gz | |||
| SRR16154100_2.fastq.gz | Fastqsanger.gz | |||
| SRR16154200_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1988 |
Similar Datasets
Project description:Genetic interactions are fundamental to the architecture of complex traits, yet the molecular mechanisms by which variant combinations influence cellular pathways remain poorly understood. Here, we answer the question of whether interactions between genetic variants can activate unique pathways and if such pathways can be targeted to modulate phenotypic outcomes. The model organism Saccharomyces cerevisiae was used to dissect how two causal SNPs , MKT189G and TAO34477C, interact to modulate metabolic and phenotypic outcomes during sporulation. By integrating time-resolved transcriptomics, absolute proteomics, and targeted metabolomics in isogenic allele replacement yeast strains, we show that the combined presence of these SNPs uniquely activates the arginine biosynthesis pathway and suppresses ribosome biogenesis, reflecting a metabolic trade-off that enhances sporulation efficiency. Functional validation demonstrates that the arginine pathway is essential for mitochondrial activity and efficient sporulation only in the double-SNP background. Our findings show how genetic variant interactions can rewire core metabolic networks, providing a mechanistic framework for understanding polygenic trait regulation and the emergence of additive effects in complex traits.
2025-07-22 | PXD056947 | Pride
Project description:Epistasis and pleiotropy are important features of the genetic architecture of quantitative traits, but are difficult to assess in outbred populations. We performed a diallel cross among Drosophila P-element mutations previously associated with hyper-aggressive behavior, and demonstrated extensive epistatic and pleiotropic effects on aggression, brain morphology, and genome wide gene expression. Epistatic interactions were often of greater magnitude than homozygous effects, and the topology of the epistatic networks varied among the traits. The transcriptional signature of the homozygous and double heterozygous genotypes derived from the six mutations implies a large mutational target size for aggressive behavior and evolutionarily conserved genetic mechanisms and neural signaling pathways affecting aggressive behavior. We used six mutant lines homozygous for a P-element insertion, the 15 possible transheterozygous combinations of the initial six lines and a control line. All lines were isogenic other than the P-element insert. three replicates were done for a total of 66 arrays
2011-10-13 | E-MTAB-653 | biostudies-arrayexpress
Project description:Transcript abundance in adipose and liver tissues was used to map expression quantitative trait loci (eQTL) underlying fat accretion, weight gain and liver weight. Gonadal fat and liver tissues were used from 48 individuals F2 selected from a cohort (1,200 mice) originated from a cross between M16i and MB2 mice. A complex polygenic architecture within the MB2 locus was observed which was comprised of several locally regulated eQTL (cis-eQTL) with significant correlations to obesity traits. Total RNA obtained from isolated gonadal fat and liver tissues were used to mesured transcript abundance in order to detect expression QTLs.
2010-09-15 | E-GEOD-20724 | biostudies-arrayexpress
Project description:Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. In the current study, systems genetics approaches were used to explore the genetic regulation of lignin traits in B. napus seeds. Four QTL (qLignin_A09_1, qLignin_A09_2, qLignin_A09_3, and qLignin_C08) distributed on two chromosomes were identified for lignin content. The qLignin_A09_2 and qLignin_C08 loci were homologous QTL from the A and C subgenomes, respectively. Genome-wide gene regulatory network analysis identified eighty-three subnetworks (or modules); and three modules with 910 genes in total, were associated with lignin content, which was confirmed by network QTL analysis. eQTL (expression quantitative trait loci) analysis revealed four cis-eQTL genes including lignin and flavonoid pathway genes, cinnamoyl-CoA-reductase (CCR1), and TRANSPARENT TESTA genes TT4, TT6, TT8, as causal genes. The findings validated the power of systems genetics to identify causal regulatory networks and genes underlying complex traits. Moreover, this information may enable the research community to explore new breeding strategies, such as network selection or gene engineering, to rewire networks to develop climate resilience crops with better seed quality.
2024-06-04 | GSE268725 | GEO
Project description:Genetic interactions are fundamental to the architecture of complex traits, yet the molecular mechanisms by which variant combinations influence cellular pathways remain poorly understood. Here, we answer the question of whether interactions between genetic variants can activate unique pathways and if such pathways can be targeted to modulate phenotypic outcomes. The model organism Saccharomyces cerevisiae was used to dissect how two causal SNPs , MKT189G and TAO34477C, interact to modulate metabolic and phenotypic outcomes during sporulation. By integrating time-resolved transcriptomics, absolute proteomics, and targeted metabolomics in isogenic allele replacement yeast strains, we show that the combined presence of these SNPs uniquely activates the arginine biosynthesis pathway and suppresses ribosome biogenesis, reflecting a metabolic trade-off that enhances sporulation efficiency. Functional validation demonstrates that the arginine pathway is essential for mitochondrial activity and efficient sporulation only in the double-SNP background. Our findings show how genetic variant interactions can rewire core metabolic networks, providing a mechanistic framework for understanding polygenic trait regulation and the emergence of additive effects in complex traits.
2025-07-22 | GSE278267 | GEO
Project description:The aim of this study was to conduct a genome-wide analysis for constituent tuber carotenoid QTL. Using a genetical genomics approach samples from clones with similar carotenoid traits were bulked and patterns of gene expression were measured for each bulk by microarray analysis. Variation of gene expression within these bulks may be due to either polymorphisms located near to or within the gene (cis-eQTL) or indirectly from a distant location on the genome (trans-eQTL). Differentially expressed clones from bulks with contrasting carotenoid traits were genetically mapped in order to re-enforce the QTL analysis, and provide a rapid means of developing gene markers closely associated with the target traits.
2011-12-26 | E-TABM-1200 | biostudies-arrayexpress
Project description:Transcript abundance in adipose and liver tissues was used to map expression quantitative trait loci (eQTL) underlying fat accretion, weight gain and liver weight. Gonadal fat and liver tissues were used from 48 individuals F2 selected from a cohort (1,200 mice) originated from a cross between M16i and MB2 mice. A complex polygenic architecture within the MB2 locus was observed which was comprised of several locally regulated eQTL (cis-eQTL) with significant correlations to obesity traits.
2010-09-15 | GSE20724 | GEO
Project description:Epistatic regulation of complex traits and gene expression in mice
| PRJNA607735 | ENA
Project description:The genomic distribution of trait-associated SNPs (TASs) discovered in genome-wide association studies (GWAS) can provide insight into the genetic architecture of complex traits and the design of future studies. Here we report on a maize GWAS that identified TASs underlying five quantitative traits measured across a large panel of samples and examine the characteristics of these TASs. A set of SNPs obtained via RNA sequencing (RNA-seq), most of which are located within annotated genes (~87%) were complemented with additional SNPs from the maize HapMap Project that contains approximately equal proportions of intragenic and intergenic SNPs. TASs were identified via a genome scan while controlling for polygenic background effects. The diverse functions of TAS-containing candidate genes indicate that complex genetic networks shape these traits. The vast majority of the TAS-containing candidate genes have dynamic expression levels among developmental stages. Overall, TASs explain 44~54% of the total phenotypic variation for these traits, with equal contributions from intra- and inter-genic TASs. Association of ligueless2 with upper leaf angle was implicated by two intragenic TASs; rough sheath1 was associated with leaf width by an upstream intergenic TAS; and Zea agamous5 was associated with days to silking by both intra- and inter-genic TASs. A large proportion (82%) of these TASs comes from noncoding regions, similar to findings from human diseases and traits. However, TASs were enriched in both intergenic (53%) and promoter 5kb (24%) regions, but under-represented in a set of nonsynonymous SNPs.
2012-06-11 | E-MTAB-4233 | biostudies-arrayexpress