Recount-genotype
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ABSTRACT:
PROVIDER: PRJNA1231607 | ENA |
REPOSITORIES: ENA
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Project description:plant genotype x rhizobium genotype interaction
| PRJNA140483 | ENA
Project description:Coevolutionary change requires reciprocal selection between interacting species, i.e., that the partner genotypes that are favored in one species depend on the genetic composition of the interacting species. Coevolutionary genetic variation is manifested as genotype ´ genotype (G ´ G) interactions for fitness from interspecific interactions. Although quantitative genetic approaches have revealed abundant evidence for G ´ G interactions in symbioses, the molecular basis of this variation remains unclear. Here we study the molecular basis of G ´ G interactions in a model legume-rhizobium mutualism using gene expression microarrays. We find that, like quantitative traits such as fitness, variation in the symbiotic transcriptome may be partitioned into additive and interactive genetic components. Our results suggest that plant genetic variation is the largest influence on nodule gene expression, and that plant genotype and the plant genotype ´ rhizobium genotype interaction determine global shifts in rhizobium gene expression that in turn feedback to influence plant fitness benefits. Moreover, the transcriptomic variation we uncover implicates regulatory changes in both species as drivers of symbiotic gene expression variation. Our study is the first to partition genetic variation in a symbiotic transcriptome, and illuminates potential molecular routes of coevolutionary change. We assayed gene expression using three biological replicates for each plant genotype × rhizobium genotype combination (4 combinations) for a total of 12 chips.
2012-05-01 | GSE29027 | GEO
Project description:Phenotype Genotype Biomarkers (PGB)
| PRJNA815694 | ENA
Project description:African American hepatocyte genotype
| PRJNA615863 | ENA
Project description:Phenotype Genotype Biomarkers (PGB)
| PRJNA815693 | ENA
Project description:imputated genotype data
| PRJEB100773 | ENA
Project description:Background For many complex diseases, including Parkinson’s disease, regulatory elements located in intergenic regions have been putatively associated with disease risk and development. However, the biological mechanisms linking these intergenic loci to disease pathogenesis remain largely unknown. Fundamentally, this is because these intergenic loci are non-coding, and bespoke approaches to in-depth functional characterisation are required. Here we utilised an integrative, functional approach to identify the genotype-specific impacts of Parkinson’s disease-associated variant rs11610045, located within a complex region on chromosome 12. Methods & Results We utilised CRISPR-Cas9 editing (and reversal) to generate isogenic iPSC clones from the KOLF2.1J line containing either the A|A (WT) or G|G (edited) rs11610045 genotype. We also reverted the G|G genotype back to the A|A genotype in two clones to control for off-target effects. Functional profiling of these clones demonstrated allele-specific regulation of both nearby and distal genes, including THBS1 and PDGFB. Further, affinity purification followed by mass spectrometry identified the differential binding of potential regulatory proteins to the G|G genotype compared to the WT A|A genotype, including the transcription factor TCF7L1. Conclusions Our findings support a model in which non-coding variants, such as rs11610045, impact the expression and downstream activity of multiple genes predominantly through trans-acting mechanisms. In so doing, this study demonstrates a pipeline to delineate SNP-specific impacts in an iPSC model. Finally, we highlight the challenge of aligning genotype dependent expectations of the impact of expression quantitative loci on genes as part of the exploration of how inherited genetic variation contributes to complex genetic disease.
2026-04-07 | PXD065108 | Pride
Project description:IL28B genotype was shown to be associated with treatment outcome of antiviral thearpy for HCV infection. We tried to clarify the molecular feature that was asocciated with IL2B genotype by comparing Hepatic gene expression of HCV related Hepatocellular carcinoma and non-cancerous tissue with Il28B rs8099917 TT genotype and TG/GG genotype.
2013-05-02 | GSE41804 | GEO
Project description:Genotype-Tissue Expression Project (GTEx)
| PRJNA158505 | ENA