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69 results for “condition-dependent”
Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network
<p>In this repository we provide raw and processed datasets for the article: “Genome-wide gene expression noise in <em>Escherichia coli </em>is condition-dependent and determined by propagation of noise through the regulatory network<strong>” </strong>by Arantxa Urchueguía, Luca Galbusera, Dany Chauvin, Gwendoline Bellement, Thomas Julou and Erik van Nimwegen.</p> <p>A preprint is available under the following DOI: <a href="https://doi.org/10.1101/795369">https://doi.org/10.1101/795369</a>. </p> <p>The repository consists of the following datasets: </p> <p><strong>1. preprocessed_datasets.zip(~22GB)</strong></p> <ul> <li>This dataset contains raw data from the flow cytometry experiments (FACS Canto II, BD Bioscience) in all measured conditions in RData format. Raw fcs files were processed with the tools described in the publication ''Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria" published here: <a href="https://doi.org/10.1371/journal.pone.0240233">https://doi.org/10.1371/journal.pone.0240233</a>. The tools themselves are available here: <a href="https://github.com/vanNimwegenLab/E-Flow">https://github.com/vanNimwegenLab/E-Flow</a>. Included in the files are the outputs of these processing tools together with all raw values that came directly from the flow cytometer. The file <em>directory_structure_in_preprocessed </em>contains information about how the files are organized.</li> </ul> <p><strong>2. info_files: </strong>This is a set of csv files containing detailed information about the experiments done to acquire the preprocessed_datasets as well as annotation files that we used to retrieve promoter information. </p> <p><strong>3. processed_datasets:</strong> These files correspond to the processed datasets from the raw Rdata files under 1 above. The processed data provide mean and variance estimates in fluorescence of E.coli promoters across the different growth conditions. Note that we discarded flow cytometry measurements from promoter/growth-condition combinations that contained abnormal fluorescence distributions (due to contamination) as well as measurements from reporters with annotation mismatches. The folder contains the following clean dataset files that were used in the paper:</p> <ul> <li><strong>FULL_dataset_mean_var_wreplicates:</strong> In this dataset we include the processed means and variances (in both logarithmic and linear scale) of all promoters in each condition. Included as well are replicate measurements for some conditions.. We also include the name and Blattner number of the gene immediately downstream of each promoter, the DNA sequence of each promoter, and regulatory information (number of unique inputs for transcription factors sites and their names) which we obtained from RegulonDB v 10.5 (<a href="https://doi.org/10.1093/nar/gky1077">https://doi.org/10.1093/nar/gky1077</a>). </li> <li><strong>dataset_with_noise_estimates: </strong>In this dataset we provide noise estimates for all promoters expressed above an expression threshold (mean GFP fluorescence at least as large as autofluorescence). Note that the noise estimate correspond to the difference between the promoter’s variance in log-expression and the minimal variance as a function of its mean expression (i.e. the so called noise floor was subtracted). Apart from the mean, variance, noise and promoter features (sequence, name of gene downstream, number of unique regulatory inputs and name of the TFs binding), we also include the parameters used for fitting the minimal noise, i.e. noise floor, in each of the conditions. </li> <li><strong>time_course_data_SI</strong>: This dataset contains mean and variance measurements of one of the plates of the library measured at different time points during growth in Minimal media 0.4M NaCl: 0h (just after dilution), 1h, 2h, 3h, 5h, 6.5h, 8.5h, 10h and 11h. </li> <li><strong>growth_curves_SI</strong>: Growth data (OD<sub>600</sub> as a function of time) for a subset of the promoters from the library across different growth conditions.</li> <li><strong>singlecell_areas_SI: </strong>Single-cell areas estimated using agar patches of cells growing in each condition. Each row of the table contains data for a single-cell. </li> <li><strong>synthetic_promoters_dataset: </strong>This dataset contains mean, variance and noise measurements of a set of constitutive promoters from <a href="https://doi.org/10.7554/eLife.05856.001">https://doi.org/10.7554/eLife.05856.001</a> across different conditions.</li> <li><strong>MARA_results:</strong> All transcription factor activities results explaining measured noise levels in each condition. This data has been obtained after performing Motif Activity Response Analysis on the noise levels of all measured promoters in each condition.</li> </ul>
Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly
<p>Condition is assumed to reflect both genes and environment, enabling condition-dependent signals to reveal genetic quality. However, because the phenotypic effects of variation in genetic quality could be masked by environmental heterogeneity, the contribution of genetic quality to phenotypic variation in fitness-related traits and condition-dependent signals remains unclear. We compared effects of ecologically relevant manipulations of environmental quality (nutrient dilution in the larval diet) and genetic quality (one generation of inbreeding) on male and female morphology, life history and reproductive performance in the neriid fly <em>Telostylinus angusticollis</em>. We found that larval diet quality had strong, positive effects on male and female body size, male secondary sexual traits, and aspects of male and female reproductive performance. By contrast, inbreeding had weak effects on most traits, and no trait showed clear and consistent effects of both environmental and genetic quality. Indeed, inbreeding effects on body size and male competitive performance were of opposite sign in rich vs. poor larval diet treatment groups. Our results suggest that environmental quality strongly affects condition, but the effects of genetic quality are subtle and environment-dependent in this species. These findings raise questions about the genetic architecture of condition and the potential for condition-dependent traits to function as signals of genetic quality.</p>
Condition-dependent sexual reproduction is driven by benefits, not costs of sex
<p>Facultative sexual organisms must allocate resources to both asexual and sexual reproduction. Optimal patterns of investment in sex depend on the relative costs and benefits of each reproductive mode, and may consequently be context- and condition-dependent. Two proposed explanations for the observed variation in investment in sex among facultative sexual lineages invoke alternative condition-dependent scenarios. Under the 'fitness-associated sex' hypothesis, sex is predicted when individuals are in poor condition or experience stressful environments. Under the 'resource-demanding sex' hypothesis, sex is only affordable to individuals in good condition experiencing favourable environments. Direct tests of these contrasting hypotheses are rare; moreover, investment in different components of sexual reproduction responds differently to cues promoting sex, and may be subject to different energetic constraints. Using genotypes of facultative sexual Daphnia carinata that differ in their level of investment in sex, we manipulated resource availability while accounting for day length (a seasonal cue for sex) to evaluate these hypotheses. The sexual response to day length depended on resource availability: increased day lengths and reduced food availability increased the production of sexual eggs, and relative investment in males, in a manner consistent with the fitness-associated sex hypothesis. The pattern of condition-dependence was specific to each component of reproductive investment – while male production covaried with asexual fecundity across genotypes, increased sexual egg production was associated with reduced asexual reproduction. Our results suggest that investment in sex is determined largely by its context-dependent advantages, and that this investment is not moderated by immediate costs to asexual reproduction.</p>
Condition-dependent sexual reproduction is driven by benefits, not costs of sex
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Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly
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The condition-dependence of male genital size and shape
<p>The male genitals of internal fertilizers evolve rapidly and divergently, and sexual selection is generally responsible for this. Many sexually selected traits are condition-dependent - with their expression dependent upon the resources available to be allocated to them - as revealed by genetic or environmental manipulations of the condition. However, it is not clear whether male genitals are also condition-dependent. Here we manipulate the condition in two ways (via inbreeding and diet) to test the condition-dependence of the genital arch of <em>Drosophila simulans</em>. We found that genital size but not genital shape suffered from inbreeding depression, whereas genital size and shape were affected by dietary manipulation of the condition. The differential effects of these treatments likely reflect the underlying genetic architecture that has been shaped by past selection: inbreeding depression is only expected when traits have a history of directional selection, while diet impacts traits regardless of historical selection. Nonetheless, our results suggest genitals can be condition-dependent like other sexually selected traits.</p>
Data from: Condition-dependent immune function in a freshwater snail revealed by stable isotopes
<p>Data are saved as a tab-delimited text file (data.txt). Each row represents one snail individual.</p> <p> </p> <p>The file has the following columns:</p> <p>infection - trematode infection (0 = no, 1 = yes)</p> <p>PO_activity - PO-like activity of haemolymph</p> <p>antibacterial_activity - antibacterial activity of haemolymph</p> <p>shell_length - shell length (mm)</p> <p>faeces - amount of produced faeces (mg)</p> <p>d15N_faeces - δ<sup>15</sup>N value of faeces</p> <p>d13C_faeces - δ<sup>13</sup>C value of faeces</p> <p>C:N_faeces - C:N ration of faeces</p> <p>d15N_tissue - δ<sup>15</sup>N value of tissue</p> <p>d13C_tissue - δ<sup>13</sup>C value of tissue</p> <p>C:N_tissue - C:N ration of tissue</p>
Data for: Offspring plumage colouration as a condition-dependent signal in the Blue Tit
<p>In many species, offspring display conspicuous colouration already early in life, even though they might be very vulnerable to predation at this stage. However, most attention has been drawn to the conspicuous plumage displayed by adult individuals in a sexual context, while other signalling functions have been explored much less. Here, we investigated whether the yellow breast plumage of blue tit (<em>Cyanistes caeruleus</em>) nestlings shows patterns of condition-dependence and hence signals individual quality, as has been described for adult birds. During three consecutive breeding seasons, we, therefore, explored the association between nestling body mass and three colour components of the yellow breast plumage (i.e., UV chroma, carotenoid chroma and total brightness), considering both within and among nest effects. Variation in carotenoid chroma was not related to body mass. However, UV chroma and total brightness varied with body mass on an among-nest level, suggesting that they might signal aspects of genetic quality or parental rearing capacity. Interestingly, we also found a within-nest effect of body mass on total brightness, suggesting that this is a good candidate for a condition-dependent signal within the family. Thus, other family members could rely on brightness to adjust their behavioural strategies, such as feeding behaviour in parents. Our study thus reveals that certain colour components of the yellow breast plumage might signal different aspects of offspring quality and they might have a correlated signalling value across life-history stages.</p>
Dataset:Female state and condition-dependent chemical signalling revealed by male choice of silk trails
<p class="MsoNormal"><span>We ask whether males of the nuptial gift-giving spider <em>Pisaura mirabilis</em> exert preferences for mates varying in their reproductive potential based on chemical information during mate search. Males were presented with binary trails consisting of silk lines and substrate-borne chemicals deposited while females were walking, from females varying in a) body condition (high vs. low), b) developmental state (subadult vs. adult) and c) mating state (unmated vs. mated). If female chemical signaling co-varies with individual state, we expect males to choose trails of females that are a) in higher body condition, indicating higher fecundity, b) adults, which can successfully reproduce, and c) unmated, to avoid sperm competition. </span><span>We show that female signaling is condition-dependent, with m</span><span>ales being</span><span> more likely to follow trails of higher body condition females, but not dependent on female mating state. Males also tended to prefer trails of adults over subadults. Choice did not depend on male individual body condition.</span></p>
Data for: Offspring plumage colouration as a condition-dependent signal in the Blue Tit
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Data from: Condition-dependent interaction between mating success and competitive fertilization success in Drosophila melanogaster
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Data from: Condition-dependent immune response in a migrating shorebird, the common snipe Gallinago gallinago
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Data from: No evidence for phenotypic condition-dependent ejaculate allocation in response to sperm competition in a seed beetle
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Dataset:Female state and condition-dependent chemical signalling revealed by male choice of silk trails
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The condition-dependence of male genital size and shape
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Model output data for "Negative density-dependent dispersal emerges from the joint evolution of density- and body condition-dependent dispersal strategies"
<p>Empirical studies have documented both positive and negative density-dependent dispersal, yet most theoretical models predict positive density dependence as a mechanism to avoid competition. Several hypotheses have been proposed to explain the occurrence of negative density-dependent dispersal, but few of these have been formally modeled. Here, we developed an individual based model of the evolution of density-dependent dispersal. This model is novel in that it considers the effects of density on dispersal directly, and indirectly through effects on individual condition. Body condition is determined mechanistically, by having juveniles compete for resources in their natal patch. We found that the evolved dispersal strategy was a steep, increasing function of both density and condition. Interestingly, although populations evolved a positive density-dependent dispersal strategy, the simulated metapopulations exhibited negative density-dependent dispersal. This occurred because of the negative relationship between density and body condition: high density sites produced low condition individuals that lacked the resources required for dispersal. Our model therefore generates the novel hypothesis that observed negative density-dependent dispersal can occur when high density limits the ability of organisms to disperse. We suggest that future studies consider how phenotype is linked to the environment when investigating the evolution of dispersal.</p>
Data from: Condition-dependent expression of carotenoid- and melanin-based plumage colour of northern flicker nestlings revealed by manipulation of brood size
Carotenoid-based colouration in feathers is widely accepted to be a reliable signal of the health of an individual, but the condition-dependence of melanin-based plumage ornaments has been highly debated. Using broods that were manipulated in size, we tested whether nutritional stress during rearing affected the carotenoid pigmentation in secondary feathers and the size, shape, and symmetry of melanin spots on breast plumage of northern flicker Colaptes auratus nestlings. Two measures of carotenoid colour (chroma and brightness) of secondary flight feathers did not vary according to brood size treatment, but in a larger dataset from the population, carotenoid chroma was positively associated with nestling mass. Nestlings from experimentally enlarged broods had smaller melanin spots than those from reduced broods, which is some of the first experimental evidence that melanin ornament size in growing nestlings is condition-dependent. However, the shape and symmetry of the melanin breast spots was not associated with nestling mass. Sexual dimorphism was apparent in both types of pigmentation and future studies should investigate whether there are any trade-offs for nestlings between investing in carotenoid colouration and melanisation and whether trade-offs differ between the sexes.
Data from: Maternal effects obscure condition-dependent sex allocation in changing environments
Climate change increases environmental fluctuations which thereby impact population demography. Species with temperature-dependent sex determination may experience more extreme sex ratio skews, but this has not been considered in species with chromosomally-determined sex. However, anticipatory maternal effects cause lifelong physiological changes impacting sex ratios. Here we show, in mice, that more sons were born to mothers in good condition when their breeding environment matched their gestational environment, consistent with theoretical predictions, but mothers in mismatched environments have no condition sex-ratio relationship. Thus, the predicted effect of condition on sex ratio was obscured by maternal effects when the environment changed. This may explain extreme or unexpected sex ratio skews in reintroduced or translocated populations, and sex ratio skews may become more common and less predictable with accelerating environmental change.
Data from: Interpopulation variation in a condition-dependent signal: predation regime affects signal intensity and reliability
In many models of sexual selection, conspicuous ornaments are preferred by mates because they indicate heritable signaler viability. To function as indicators, ornaments must exhibit a proportional relationship between expression and viability. In cases where the evolutionary interests of signaler and receiver diverge, selection favors exploitative exaggeration by low-viability individuals producing unreliable signals. Theory suggests that the evolutionary stability of such communication systems requires costs that prevent low-viability males from expressing disproportionately intense signals. Therefore, given ecological variation in signaling cost, the reliability of signaling systems will vary concomitantly. In this study, we assess the effect of a variable signal cost, predation, on signal intensity and reliability among 16 populations of Bahamas mosquitofish (Gambusia hubbsi) that use colorful dorsal fins in courtship displays. We found that fin coloration was more intense in low-predation sites and could be used to predict body condition. However, this predictive relationship was apparent only in populations subject to predation risk. We demonstrate an important role for ecological signaling cost in communication and show that ecological heterogeneity drives interpopulation variation in both the intensity and the reliability of a sexual signal.
Data from: Condition-dependent trade-offs between sexual traits, body condition and immunity: the effect of novel habitats
Background: The optimal allocation of resources to sexual signals and other life history traits is usually dependent on an individual's condition, while variation in the expression of sexual traits across environments depends on the combined effects of local adaptation, mean condition, and phenotypic responses to environment-specific cues that affect resource allocation. A clear contrast can often be drawn between natural habitats and novel habitats, such as forest plantations and urban areas. In some species, males seem to change their sexual signals in these novel environments, but why this occurs and how it affects signal reliability is still poorly understood. Results: The relative size of sexual traits and level of immune responses were significantly lower for male palmate newts Lissotriton helveticus caught in pine and eucalyptus plantations compared to those caught in native forests, but there was no habitat-dependent difference in body condition (n= 18 sites, 382 males). The reliability with which sexual traits signalled body condition and immune responses was the same in all three habitats. Finally, we conducted a mesocosm experiment in which males were maintained in pine, eucalypt or oak infused water for 21 days. Males in plantation-like water (pine or eucalypt) showed significantly lower immune responses but no change in body condition. This matches the pattern seen for field-caught males. Unlike field-caught males, however, there was no relationship between water type and relative sexual trait size. Conclusions: Pine and eucalyptus plantations are likely to be detrimental to male palmate newt because they are associated with reduced immune function and smaller sexual traits. This could be because ecological aspects of these novel habitats, such as high water turbidity or changes in male-male competition, drive selection for reduced investment into sexual traits. However, it is more probable that there are differences in the ease of acquisition, hence optimal allocation, of resources among habitats. Our mesocosm experiment also provides some evidence that water toxicity is a causal factor. Our findings offer insights into how plantations affect amphibian life histories, and how novel habitats might generate long-term selection for new resource allocation strategies in native species.
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