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Dataset results
44 results for “QTLs”
Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach
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Data from: Young inversion with multiple linked QTLs under selection in a hybrid zone
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Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans
The pig is a well-known animal model used to investigate genetic and mechanistic aspects of human disease biology. They are particularly useful in the context of obesity and metabolic diseases because other widely used models (e.g. mice) do not completely recapitulate key pathophysiological features associated with these diseases in humans. Therefore, we established a F2 pig resource population (n = 564) designed to elucidate the genetics underlying obesity and metabolic phenotypes. Segregation of obesity traits was ensured by using breeds highly divergent with respect to obesity traits in the parental generation. Several obesity and metabolic phenotypes were recorded (n = 35) from birth to slaughter (242 ± 48 days), including body composition determined at about two months of age (63 ± 10 days) via dual-energy x-ray absorptiometry (DXA) scanning. All pigs were genotyped using Illumina Porcine 60k SNP Beadchip and a combined linkage disequilibrium-linkage analysis was used to identify genome-wide significant associations for collected phenotypes. We identified 229 QTLs which associated with adiposity- and metabolic phenotypes at genome-wide significant levels. Subsequently comparative analyses were performed to identify the extent of overlap between previously identified QTLs in both humans and pigs. The combined analysis of a large number of obesity phenotypes has provided insight in the genetic architecture of the molecular mechanisms underlying these traits indicating that QTLs underlying similar phenotypes are clustered in the genome. Our analyses have further confirmed that genetic heterogeneity is an inherent characteristic of obesity traits most likely caused by segregation or fixation of different variants of the individual components belonging to cellular pathways in different populations. Several important genes previously associated to obesity in human studies, along with novel genes were identified. Altogether, this study provides novel insight that may further the current understanding of the molecular mechanisms underlying human obesity.
Data from: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes
Previous studies had shown that integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals both local and trans expression Quantitative Trait Loci (eQTLs) demonstrating 2 trans eQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provides a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.
Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans
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Data from: Body composition QTLs identified in intercross populations are reproducible in consomic mouse strains
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Correlation and co-localization of QTLs for stomatal density, canopy temperature, and productivity with and without drought stress in Setaria
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Data from: Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms
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Data from: Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes
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RNA Expression QTL mapping in an F2 cross of BALB/cJ and BALB/cByJ mice to identify candidate genes for behavioral/metabolic QTLs
GEO Series GSE196334. Mus musculus. 64 samples. Type: Expression profiling by high throughput sequencing.
Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress
GEO Series GSE220996. Oryza sativa. 8 samples. Type: Expression profiling by high throughput sequencing.
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.
GEO Series GSE116193. Homo sapiens. 112 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Discovery and characterization of variance QTLs in human induced pluripotent stem cells
GEO Series GSE118723. Homo sapiens. 7584 samples. Type: Expression profiling by high throughput sequencing; Other.
CAST x C57 QTLs Effect on Gene Expression for Chromosomes 2, 11, and 17
GEO Series GSE22042. Mus musculus. 72 samples. Type: Expression profiling by array.
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-array]
GEO Series GSE57481. Homo sapiens. 64 samples. Type: Methylation profiling by genome tiling array.
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels [Bisulfite-Seq]
GEO Series GSE57471. Homo sapiens. 10 samples. Type: Methylation profiling by high throughput sequencing.
RNA Expression QTL mapping in Striatum of an F2 cross of BALB/cJ and BALB/cByJ mice to identify candidate genes for behavioral/metabolic QTLs
GEO Series GSE196352. Mus musculus. 64 samples. Type: Expression profiling by high throughput sequencing.
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels
GEO Series GSE57483. Homo sapiens. 74 samples. Type: Methylation profiling by genome tiling array; Methylation profiling by high throughput sequencing.
Modulation of apple leaf transcriptome by QTLs and infection by Venturia inaequalis
GEO Series GSE250309. Malus domestica. 16 samples. Type: Expression profiling by high throughput sequencing.
A global analysis of QTLs for expression variations in rice flag leaf at heading date
GEO Series GSE49020. Oryza sativa. 216 samples. Type: Expression profiling by array.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.