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1,363 results for “phenotypic data”
Data from: A new phylogenetic method for identifying exceptional phenotypic diversification
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Data from: Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk
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F2833 scRNA-seq data for manuscript "Therapeutic vaccine containing a novel liposomal adjuvant shifts pathogenic Th17 cells into a Tr1-like phenotype"
GEO Series GSE240801. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system, postimmunization expression data.
GEO Series GSE98589. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome data - Respiratory S. cerevisiae Strain Phenotype is Glucose Insensitive and vital TFs are Hap4 Cat8 Mig1
GEO Series GSE11799. Saccharomyces cerevisiae. 24 samples. Type: Expression profiling by array.
Brain transcriptional and epigenetic associations with the autistic phenotype (methylation data)
GEO Series GSE38608. Homo sapiens. 36 samples. Type: Methylation profiling by array.
F2702 bulk RNA-seq data for manuscript "Therapeutic vaccine containing a novel liposomal adjuvant shifts pathogenic Th17 cells into a Tr1-like phenotype"
GEO Series GSE240800. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system, blood monocyte and brain microglia expression data
GEO Series GSE107790. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Prediction of antibiotic resistance by large-scale phenotypic and genotypic data
GEO Series GSE59408. Escherichia coli. 42 samples. Type: Expression profiling by array.
Genomic and phenotypic stability of fusion-driven pediatric sarcoma cell lines [Infinium genotyping data]
GEO Series GSE270195. Homo sapiens. 29 samples. Type: Genome variation profiling by genome tiling array.
Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system, peak of disease expression data
GEO Series GSE107791. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
The Effect of Adolescent Environmental Enrichment and Social Defeat on the Nucleus Accumbens and Hippocampus in a Selectively Bred Model with Anxious Phenotype (bLR Rats): RNAseq data
GEO Series GSE237890. Rattus norvegicus. 80 samples. Type: Expression profiling by high throughput sequencing.
Extended data for publication "Dictionary of disease ontologies (DODO): a graph database to facilitate access and interaction with disease and phenotype ontologies"
<p>This archive contains the extended data for the publication "Dictionary of disease ontologies (DODO): a graph database to facilitate access and interaction with disease and phenotype ontologies". This includes two sheet within the "ExtendedData.xlsx" file:</p> <p>Table1: List of all functions available in DODO R package with description and scope details.<br> Table2: List of ontologies among which the cross-reference relations are encoded as is_xref</p> <p>Data are available under the terms of the <a href="http://creativecommons.org/publicdomain/zero/1.0/">Creative Commons Zero "No rights reserved" data waiver</a> (CC0 1.0 Public domain dedication).</p>
Data from: Genetic divergence and phenotypic plasticity contribute to variation in cuticular hydrocarbons in the seaweed fly Coelopa frigida
Cuticular hydrocarbons (CHCs) form the boundary between insects and their environments and often act as essential cues for species, mate and kin recognition. This complex polygenic trait can be highly variable both among and within species, but the causes of this variation, especially the genetic basis, are largely unknown. In this study, we investigated phenotypic and genetic variation of CHCs in the seaweed fly, C. frigida, and found that composition was affected by both genetic (sex and population) and environmental (larval diet) factors. We subsequently conducted behavioral trials that show CHCs are likely used as a sexual signal. We identified general shifts in CHC chemistry as well as individual compounds and found that the methylated compounds, mean chain length, proportion of alkenes, and normalized total CHCs differed between sexes and populations. We combined this data with whole genome re-sequencing data to examine the genetic underpinnings of these differences. We identified 11 genes related to CHC synthesis and found population level outlier SNPs in 5 that are concordant with phenotypic differences. Together these results reveal that the CHC composition of C. frigida is dynamic, strongly affected by the larval environment, and likely under natural and sexual selection.
Data from: Effective polyploidy causes phenotypic delay and influences bacterial evolvability
Whether mutations in bacteria exhibit a noticeable delay before expressing their corresponding mutant phenotype was discussed intensively in the 1940s to 1950s, but the discussion eventually waned for lack of supportive evidence and perceived incompatibility with observed mutant distributions in fluctuation tests. Phenotypic delay in bacteria is widely assumed to be negligible, despite the lack of direct evidence. Here, we revisited the question using recombineering to introduce antibiotic resistance mutations into E. coli at defined time points and then tracking expression of the corresponding mutant phenotype over time. Contrary to previous assumptions, we found a substantial median phenotypic delay of three to four generations. We provided evidence that the primary source of this delay is multifork replication causing cells to be effectively polyploid, whereby wild-type gene copies transiently mask the phenotype of recessive mutant gene copies in the same cell. Using modeling and simulation methods, we explored the consequences of effective polyploidy for mutation rate estimation by fluctuation tests and sequencing-based methods. For recessive mutations, despite the substantial phenotypic delay, the per-copy or per-genome mutation rate is accurately estimated. However, the per-cell rate cannot be estimated by existing methods. Finally, with a mathematical model, we showed that effective polyploidy increases the frequency of costly recessive mutations in the standing genetic variation (SGV), and thus their potential contribution to evolutionary adaptation, while drastically reducing the chance that de novo recessive mutations can rescue populations facing a harsh environmental change such as antibiotic treatment. Overall, we have identified phenotypic delay and effective polyploidy as previously overlooked but essential components in bacterial evolvability, including antibiotic resistance evolution.
Data from: Among-sibling differences in the phenotypes of juvenile fish depend on their location within the egg mass and maternal dominance rank
We investigated whether among-sibling differences in the phenotypes of juvenile fish were systematically related to the position in the egg mass where each individual developed during oogenesis. We sampled eggs from the front, middle and rear thirds of the egg mass in female brown trout of known dominance rank. In the resulting juveniles, we then measured traits that are related to individual fitness: body size, social status and standard metabolic rate (SMR). When controlling for differences among females in mean egg size, siblings from dominant mothers were initially larger (and had a lower mass-corrected SMR) if they developed from eggs at the rear of the egg mass. However, heterogeneity in the size of siblings from different positions in the egg mass diminished in lower ranking females. Location of the egg within the egg mass also affected the social dominance of the resulting juvenile fish, although the direction of this effect varied with developmental age. This study provides the first evidence of a systematic basis for among-sibling differences in the phenotypes of offspring in a highly fecund organism.
Data from: The genetics of phenotypic plasticity. XII. Temporal and spatial heterogeneity
In order to understand empirical patterns of phenotypic plasticity, we need to explore the complexities of environmental heterogeneity and how it interacts with cue reliability. I consider both temporal and spatial variation separately and in combination, the timing of temporal variation relative to development , the timing of movement relative to selection, and two different patterns of movement: stepping-stone and island. Among-generation temporal heterogeneity favors plasticity, while within-generation heterogeneity can result in cue unreliability. In general, spatial variation more strongly favors plasticity than temporal variation, and island migration more strongly favors plasticity than stepping-stone migration. Negative correlations among environments between the time of development and selection can result in seemingly maladaptive reaction norms. The effects of higher dispersal rates depends on the life history stage when dispersal occurs and the pattern of environmental heterogeneity. Thus, patterns of environmental heterogeneity can be complex and can interact in unforeseen ways to affect cue reliability. Proper interpretation of patterns of trait plasticity require consideration of the ecology and biology of the organism. More information on actual cue reliability and the ecological and developmental context of trait plasticity is needed.
Data from: Phenotypic plasticity in female mate choice behavior is mediated by an interaction of direct and indirect genetic effects in Drosophila melanogaster
Female mate choice is a complex decision-making process that involves many context-dependent factors. In Drosophila melanogaster, a model species for the study of sexual selection, indirect genetic effects (IGEs) of general social interactions can influence female mate choice behaviors, but the potential impacts of IGEs associated with mating experiences are poorly understood. Here, we examined whether the IGEs associated with a previous mating experience had an effect on subsequent female mate choice behaviors and quantified the degree of additive genetic variation associated with this effect. Females from 21 different genetic backgrounds were housed with males from one of two distinct genetic backgrounds for either a short (3 hr) or long (48 hr) exposure period and their subsequent mate choice behaviors were scored. We found that the genetic identity of a previous mate significantly influenced a female's subsequent interest in males and preference of males. Additionally, a hemiclonal analysis revealed significant additive genetic variation associated with experience-dependent mate choice behaviors, indicating a genotype-by-environment interaction for both of these parameters. We discuss the significance of these results with regard to the evolution of plasticity in female mate choice behaviors and the maintenance of variation in harmful male traits.
Data from: Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: the Latent Environmental Threshold Model
Conditional strategies are the most common form of discrete phenotypic plasticity. In a conditional strategy, the phenotype expressed by an organism is determined by the difference between an environmental cue and a threshold, both of which may vary among individuals. The Environmental Threshold model (ETM) has been proposed as a mean to understand the evolution of conditional strategies, but has been surprisingly seldom applied to empirical studies. A hindrance for the application of the ETM is that often, the proximate cue triggering the phenotypic expression and the individual threshold are not measurable, and can only be assessed using a related observable cue. We describe a new statistical model that can be applied in this common situation. The Latent Environmental Threshold Model (LETM) allows for a measurement error in the phenotypic expression of the individual environmental cue and a purely genetically determined threshold. We show that coupling our model with quantitative genetic methods allows an evolutionary approach including an estimation of the heritability of conditional strategies. We evaluate the performance of the LETM with a simulation study and illustrate its utility by applying it to empirical data on the size-dependent smolting process for stream-dwelling Atlantic salmon juveniles.
Data from: The impact of bottlenecks on microbial survival, adaptation and phenotypic switching in host-pathogen interactions
Microbial pathogens and viruses can often maintain sufficient population diversity to evade a wide range of host immune responses. However, when populations experience bottlenecks, as occurs frequently during initiation of new infections, pathogens require specialized mechanisms to regenerate diversity. We address the evolution of such mechanisms, known as stochastic phenotype switches, which are prevalent in pathogenic bacteria. We analyze a model of pathogen diversification in a changing host environment that accounts for selective bottlenecks, wherein different phenotypes have distinct transmission probabilities between hosts. We show that under stringent bottlenecks, such that only one phenotype can initiate new infections, there exists a threshold stochastic switching rate below which all pathogen lineages go extinct, and above which survival is a near certainty. We determine how quickly stochastic switching rates can evolve by computing a fitness landscape for the evolutionary dynamics of switching rates, and analyzing its dependence on both the stringency of bottlenecks and the duration of within-host growth periods. We show that increasing the stringency of bottlenecks or decreasing the period of growth results in faster adaptation of switching rates. Our model provides strong theoretical evidence that bottlenecks play a critical role in accelerating the evolutionary dynamics of pathogens.
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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.