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4,120 results for “sex”
Data for: Cephalopod Sex Determination and its Ancient Evolutionary Origin
<p>This repository contains the chromosome-level genome assembly, annotation, and genome hub files of the California two-spot octopus (<em>Octopus bimaculoides</em>). These data resulted in the discovery of the cephalopod sex chromosomes. Read the paper in <em>Current Biology </em>here: https://doi.org/10.1016/j.cub.2025.01.005. </p>
Weight, sex, age, beam diameter, antler points and teat length for harvested deer from 1984-2025 in Black Rock Forest, Cornwall, NY.
Data from white-tailed deer harvested within Black Rock Forest, Cornwall, New York are collected annually. Trained staff measure mass, antler beam diameter, and teat length (since 2010), estimate age via dentition, count antler points, and assess sex on all field-dressed deer. Heart girth, measured as chest circumference, was recorded from 1984 to 1998.
Data from: Sex-specific recombination landscape in a species with holocentric chromosomes
<p>Male and female meiosis typically exhibit significant differences in crossover locations along chromosomes. It has been suggested that higher recombination rates at chromosome centers in females counteract centromere-associated meiotic drivers, increasing their chances of segregating into the oocyte rather than to the non-viable polar bodies. Our research, employing the first sex-specific recombination map for an organism lacking defined centromeres revealed parallel recombination landscapes across the sexes, supporting the meiotic drive hypothesis.</p>
Dataset - Sex and Habitat effects on Verrallia aucta parasitism in Philaenus spumarius in Scotland
<p>This csv file contains data for analysis on the sex and habitat effects on <i>Verrallia aucta</i> parasitism in <i>Philaenus spumarius</i> in Scotland. <i>P. spumarius</i> were sampled from three different habitat types within eleven sites across Scotland and molecularly screened for <i>V. aucta</i> parasitism using qPCR. Csv file contains total number of <i>P. spumarius </i>samples, total number of <i>V. aucta </i>positive <i>P. spumarius </i>samples and percent positive, per sex and habitat, within each site.</p>
GWAS Summary Statistics from "Sex and statin-related genetic associations at the PCSK9 gene locus – results of genome-wide association meta-analysis"
<p>GWAMA summary statistics of PCSK9 levels stratified by sex and statin useage in Europeans.</p> <p>When using this data, please cite:</p> <p>Pott, J., Kheirkhah, A., Gadin, J.R. <em>et al.</em> Sex and statin-related genetic associations at the <em>PCSK9</em> gene locus: results of genome-wide association meta-analysis. <em>Biol Sex Differ</em> <strong>15</strong>, 26 (2024). https://doi.org/10.1186/s13293-024-00602-6</p> <p>All txt files contain the following columns:</p> <ul> <li>markername (unique SNP ID)</li> <li>chr</li> <li>bp_hg19 (base position according to hg19)</li> <li>EA (effect allele)</li> <li>OA (other allele)</li> <li>EAF (effect allele frequency)</li> <li>info (minimal info score across all used studies)</li> <li>nSamples (sample size per SNP)</li> <li>nStudies (in case of double-stratified data: number of studies; in case of single-stratified data: 2, as it is a meta-analysis of the two double-stratified data sets)</li> <li>beta (effect estimate)</li> <li>SE (standard error)</li> <li>pval (p-value)</li> <li>I2 (SNP heterogeneity across studies)</li> <li>invalidAssoc (TRUE/FALSE flag if this variant was excluded in our analysis)</li> <li>reason4exclusion (reason why this SNP was excluded)</li> <li>phenotype (phenotyp setting)</li> </ul>
Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus
<p>This is supplementary data and source data for the manuscript, <em>"Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus"</em>.</p> <p><strong>Abstract</strong>: Schizophrenia is a complex neuropsychiatric disorder with sexually dimorphic features, including differential symptomatology, drug responsiveness, and male incidence rate. Prior large-scale transcriptome analyses for sex differences in schizophrenia have focused on the prefrontal cortex. Analyzing BrainSeq Consortium data (caudate nucleus: n=399, dorsolateral prefrontal cortex: n=377, and hippocampus: n=394), we identified 831 unique genes that exhibit sex differences across brain regions, enriched for immune-related pathways. We observed X-chromosome dosage reduction in the hippocampus of male individuals with schizophrenia. Our sex interaction model revealed 148 junctions dysregulated in a sex-specific manner in schizophrenia. Sex-specific schizophrenia analysis identified dozens of differentially expressed genes, notably enriched in immune-related pathways. Finally, our sex-interacting expression quantitative trait loci analysis revealed 704 unique genes, nine associated with schizophrenia risk. These findings emphasize the importance of sex-informed analysis of sexually dimorphic traits, inform personalized therapeutic strategies in schizophrenia, and highlight the need for increased female samples for schizophrenia analyses.</p>
Island-specific evolution of a sex-primed autosome in the planarian Schmidtea mediterranea
<p>The sexual strain of the planarian <em>Schmidtea mediterranea </em>is a hermaphrodite indigenous to Tunisia and several Mediterranean islands. Here, we isolated individual chromosomes and used sequencing, Hi-C and linkage mapping to assemble a chromosome-scale genome reference. The linkage map revealed an extremely low rate of recombination on chromosome 1. We confirmed suppression of recombination on chromosome 1 by genotyping of individual sperm and oocytes. We showed that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding comprise essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicated that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We found that most known master regulators of the reproductive system are located on chromosome 1. We used RNA interference to knock down a gene with haplotype-biased expression and observed that this led to the formation of a more pronounced female mating organ. Based on these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome.</p>
E4warning_2020_Population_Age_Sex
<p>Worldpop Human 2020 population by Age and Gender. </p> <p>Abstract: Human population estimates per pixel were extracted from MOOD partner Worldpop (www.worldpop.org) datasets for the MOOD extent. Gender age categories were summed to provide datasets for all males and all females as well as total populations. Filenames are are follows (MOWPGGGRRYY-OOCog.TIF where GGG =-gender (male = MAL, female = FEM), both = TOT); RR = Greater than (gt) or Less than (lt); YY = minimum age; OO= Maximum age</p>
Mapping of multiple complementary sex determination loci in a parasitoid wasp
<p>Files required to reproduce the analysis from the manuscript "Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp" published in Genome Biology and Evolution (doi: 10.1093/gbe/evz219). The code is hosted on the github repository CSD_lfabarum github repository (https://github.com/cmdoret/CSD_lfabarum.</p>
PWAS Hub: exploring gene-based associations of complex diseases with sex dependency - backing data
<p>The contents of the PWAS database is presented on <a title="The PWAS hub" href="https://pwas.huji.ac.il/?ver=2" target="_blank" rel="noopener">pwas.huji.ac.il</a>. The frontend and backend were build on top of a dynamical databse system. Please consult the direct API for PWAS if you wish to query the database directly: <a title="The PWAS API" href="https://pwas.huji.ac.il/API?ver=2" target="_blank" rel="noopener">pwas.huji.ac.il/API</a></p> <p>This is a PostgreSQL dump file that was created using <code>pg_dump</code>, the backup/restore procedure for PostgreSQL. To restore this into PostgreSQL do</p> <p>[a] create a database</p> <p><code>createdb DATABASE</code></p> <p>[b] on the terminal run</p> <p><code>pg_restore -vcC -h HOST -p PORT -d DATABASE < pwas_dump.20220628.psql</code></p> <p>The HOST and PORT are determined by your installation and DATABASE is given by you in step [a] abobe.</p> <p> </p> <p>To access the PWAS tables, look for table names that begin with <code>pwasAPI_</code></p> <p>A possible query to the database may look like this:</p> <p><code>SELECT * FROM "pwasAPI_genediseasestatpwas" WHERE uniprot_id = 'P09914' AND disease = 'C44';</code></p> <p>This query lists the data that associate uniprot id <strong>P09914</strong> (gene symbol IFIT1) and disease ICD-10 <strong>C44</strong> (Other malignant neoplasms of skin)</p>
Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system
<p><em>Schistosoma mansoni </em>has a diploid genome of approximately 380 MB, organized in 7 pairs of autosomes and 2 sex chromosomes. The original <em>Schistosoma mansoni </em>Genome Project was completed by the Wellcome Sanger Institute in collaboration with The Institute for Genome Research using a Whole Genome Shotgun sequencing strategy. The draft assembly was subsequently improved first by incorporating Illumina reads from a clonal (single-miracidial) infection and more recently by incorporating long PacBio reads, HiC, and optical mapping data.</p> <p>Associated manuscript can be found at https://www.biorxiv.org/content/10.1101/2021.08.13.456314v1</p>
Sex-specific relationships between urbanization, parasitism, and plumage coloration in house finches
Historically, studies of condition-dependent signals in animals have been male-centric, but recent work suggests that female ornaments can also communicate individual quality (e.g., disease state, fecundity). There also has been a surge of interest in how urbanization alters signaling traits, but we know little about if and how cities affect signal expression in female animals. We present data of carotenoid-based plumage coloration and coccidian (Isospora spp.) parasite burden in desert and city populations of house finches Haemorhous mexicanus to examine links between urbanization, health state, and feather pigmentation in males and females. In earlier work, we showed that male house finches are less colorful and more parasitized in the city, and we again detected such patterns in this study for males; however, urban females were less colorful, but not more parasitized, than rural females. Moreover, contrary to rural populations, we found that urban birds (regardless of sex) with larger patches of carotenoid coloration were also more heavily infected with coccidia. These results show that urban environments can disrupt condition-dependent color expression and highlight the need for more studies on how cities affect disease and signaling traits in both male and female animals.
Data and code from "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" Kaiser et al. 2023 Behavioral Ecology and Sociobiology
This dataset is published in support of "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" by Kaiser et al. 2023 in Behavioral Ecology and Sociobiology. Data and code to test the assumptions and key predictions of the Trivers-Willard hypothesis, which proposes that females produce more sons or daughters depending on food availability, in the black-throated blue warbler at the Hubbard Brook Experimental Forest, NH, 2007-2012. Datasets support analyses of sex ratio bias at both the nest and nestling levels. Data tables support the comparison of the ratio of variances in the scaled pre-fledging mass of male and female nestlings using an F test and reproduction of Figures 2a and 2b. Figures are those used in the published manuscript. Code supports the calculation of offspring sex ratio bias at the population level, and considering separately both low- and high-quality habitats, using the Neuhäuser test, statistical models testing the assumptions of the Trivers-Willard hypothesis, effects of food availability and parental provisioning on offspring sex ratio, and effects of food availability on pre-fledging nestling mass of sons and daughters, and a power analysis to determine the power to detect an effect of food supplementation on sex ratio. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the US Forest Service, Northern Research Station.
Sex differences in visuomotor tracking
<p>This excel file contains individual data from two cohorts presented in our publication. </p> <p>Each excel sheet presents a separate portion of data (=>one sheet per figure)</p>
Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site
<p>Metabolomics dataset used in the publication "Modeling the metabolic profile of Mytilus edulis reveals molecular signatures linked to gonadal development, sex and environmental site"</p> <p>Jaanika Kronberg, Jonathan J. Byrne, Jeroen Jansen, Philipp Antczak, Adam Hines, John Bignell, Ioanna Katsiadaki, Mark R. Viant and Francesco Falciani </p> <p>Metabolomics dataset for metabolic bins 1 to 1045 for 376 mussels as used in the publication.</p> <p>Mussel metadata are described in a separate file (spectrum number, sample label, sex, site, species, month, temperature of water, salinity of water, ADG rate, gonadal stage, parasite load)</p> <p>Species 1: Mytilus edulis, species 2: hybrid, species 3: Mytilus galloprovincialis</p>
Plotting sex differences in global causes of morbidity
<p>Data, code and graphics for causes of disability-adjusted life-years globally, separated by sex and by age-group. Data was downloaded from the World Health Organisation, 2012 records. This was used in a commissioned review article for eLS http://www.els.net/WileyCDA/ , Gilks, William P (October 2016) Sex Differences in Disease Genetics. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0026936 and is also available as an unreviewed, un-edited pre-print on bioarxiv http://dx.doi.org/10.1101/063651 http://biorxiv.org/content/early/2016/07/13/063651</p>
Plotting sex differences in genetics of waist-hip ratio
<p>For plotting results of genome-wide association study results on waist-hip ratio, originally by Shungin et al 2015 doi: 10.1038/nature14132, to be used in a commissioned review article for eLS http://www.els.net/WileyCDA/ , to be published soon, and currently available as an unreviewed, un-edited pre-print on bioarxiv http://dx.doi.org/10.1101/063651</p>
Chronic Ethanol Exposure Produces Sex-Dependent Impairments in Value Computations in the Striatum
<div> <div>These datasets and scripts are organized by figures. All data are stored as .mat format and can be open and manipulated using MATLAB. Scripts are all written in MATLAB and can be ran in MATLAB.</div> <div>There are two ways to run the code to reproduce each figures and statistics.</div> <div>1. Run RUN_ME.m. In this case, the file will automatically excute scripts to load corresponding data and figures.</div> <div>2. Open individual script to load corresponding data and generate statistics and figures.</div> <br> <div>All scripts here have been validated and tested. The system and coding environment is:</div> <div>- Windows 11 24H2</div> <div>- MATLAB 2023a</div> <br> <div>Matlab dependent package (not all are required but those are installed in my environment):</div> <div>- Bioinformatics Toolbox v4.17</div> <div>- Communications Toolbox v8.0</div> <div>- Computer Vision Toolbox v10.4</div> <div>- Curve Fitting Toolbox v3.9</div> <div>- Data Acquisition Toolbox v4.7</div> <div>- Database Toolbox v11.0</div> <div>- Deep Learning HDL Toolbox v1.5</div> <div>- Deep Learning Toolbox v14.6</div> <div>- DSP HDL Toolbox v1.2</div> <div>- Econometrics Toolbox v6.2</div> <div>- Financial Toolbox v6.5</div> <div>- Fixed-point Designer v7.6</div> <div>- Image Processing Toolbox v11.7</div> <div>- MATLAB Coder v5.6</div> <div>- MATLAB Compiler v8.6</div> <div>- MATLAB Compiler SDK v7.2</div> <div>- MATLAB Report Generator v5.14</div> <div>- MATLAB Support for MinGW-w64 C/C++ Compiler v23.1.0</div> <div>- Optimization Toolbox v9.5</div> <div>- Parallel Computing Toolbox v9.5</div> <div>- FR Toolbox v4.5</div> <div>- Signal Integrity Toolbox v1.3</div> <div>- Simulink v10.7</div> <div>- Statistics and Machine Learning Toolbox v12.5</div> <div>- Symbolic Math Toolbox v9.3</div> <div>- Text Analytics Toolbox v1.10</div> <div>- Wavelet Toolbox v6.3</div> </div>
Data from: Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus
<p>This dataset contains the sequences of Paranthropus robustus, first described in 'Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus', as well as the reference data and all the results from the analysis of those sequences.</p> <p><strong>Folders and Sub-Folders:</strong></p> <p><strong>- Paranthropus_Raw_AA_Sequences_Unaligned: </strong>Contains 2 fasta files. Paranthropus_Unaligned.fasta contains all the Paranthropus robustus sequences that were used for all of the analyses. Paranthropus_Unaligned_UNFILTERED.fasta contains all the Paranthropus robusts sequences <strong>before </strong><strong>filtering </strong>for SAP quality/confidence. These sequences were not used in any of the analyses, but are provided here for openness. </p> <p> </p> <p> </p> <p><strong>-</strong> <strong>Reference_Datasets</strong>: Contains 3 fasta files. Each fasta file is a reference dataset used in at least one analysis. The identity and origin of each sample is described in the supplementary document of the publication.</p> <p> </p> <p> </p> <p><strong>- Phylogenetic_Analysis_Datasets_and_Trees: </strong>Contains the following <strong>five folders</strong></p> <p> - <strong>Paranthropus_Alignments_All_Datasets</strong>: Contains three folders. Each folder contains the aligned and I/L corrected MSAs (Multiple Sequence Alignments) of Paranthropus robustus and a reference dataset.</p> <p> - <strong>Paranthropus_Diversity_Dataset_Trees_Results</strong>: Contains all analysis done using the 'diversity' reference dataset. Contains one folder for each protein, which includes the protein alignment and the phylogenetic tree of that protein. Additionally a folder named 'CONCATENATED' contains the concatenated alignemnts and trees. The BEAST2-STARBEAST3 folder contains the Starbeast3 analysis, including the xml, output log file, output trees and the input taxon set file.</p> <p> - <strong>Paranthropus_Representative_Dataset_Trees_Results:</strong> Contains all analysis done using the 'representative' reference dataset. Contains one folder for each protein, which includes the protein alignment and the phylogenetic tree of that protein. Additionally a folder named 'CONCATENATED' contains the concatenated alignemnts and trees. The BEAST2 folder contains the time-calibrated BEAST2 analysis, including the xml, output log file, output trees. The folder Distance_Matrix contains the generated distance matrix and the Rscript used to generate the heatmap from it.</p> <p> - <strong>Paranthropus_Independent_Dataset_Trees_Results: </strong>Contains all nexus files and tree-figures used in the analysis of the 'independent' reference dataset. </p> <p> - <strong>Tree_Figures: </strong>Contains three sub-folders and an additional figure. Each sub-folder contains the phylogenetic tree figures generated using one of the three reference datasets.</p>
Disentangling the effects of jasmonate and tissue loss on the sex allocation of an annual plant
<p>In this study, we explored norms of reaction in sex expression and sex allocation to herbivory in an experiment designed to uncouple its direct (through tissue loss) and indirect effects (due to defensive jasmonate signalling) in hermaphroditic XX females of the wind-pollinated Mercurialis annua. To uncouple the direct and indirect effects of herbivory on the sex expression and to test the role of jasmonate on conditional sex allocation, we conducted a two-factorial experiment manipulating tissue loss (25% chronic defoliation) and plant anti-herbivore defences via the jasmonate pathway (external application of jasmonate), and measured sexual expression in plants with both a male and a female function. The herbivory treatment applied were:</p> <p>For the control treatment (C), leaves were sprayed with a sham solution containing only water and polysorbate until all leaves were wet (see Supplementary Materials for detailed solution formulae). The herbivory treatment (H) consisted of cutting off half of every second leaf on the plant with scissors and spraying plants with a sham solution until all leaves were wet (defoliation resulted in a 25% reduction of total leaf area over the course of the whole plant’s lifetime). In the jasmonate treatment (JA) plants were sprayed with a solution of methyl-jasmonate and polysorbate until all leaves were wet (polysorbate 20 was used to fix the methyl-jasmonate on the sprayed leaves). Finally, the jasmonate and herbivory treatment (JAH) consisted of cutting off half of every other leaf on the plant with scissors and spraying plants with the methyl-jasmonate solution until all leaves were wet. These treatments were applied repeatedly as plants continued to grow, i.e., they represent chronic stress or manipulation. The first round of treatment was applied one week after repotting the plants (25th of November 2019) and then every two weeks over the next 12 weeks (the last treatment was applied on the 2<sup>nd</sup> of February 2020). On the first round of treatment, when most plants had fewer than six leaves each, we cut off only half a leaf (~10% of the leaf area removed) for plants under the herbivory treatments to avoid seedlings death.</p> <p>Plant sampling consisted of cutting all above-ground plant material of 34 plants per enclosure (<em>N</em> = 272) and recording total height. Plants were then cut in half, lengthwise, creating two distinct segments: top and bottom. The top segment was carefully examined and we counted the number of fruits (immature and mature) and harvested all male flowers using tweezers. Male flowers were stored in paper envelopes, dried and weighed. After phenotyping, plant segments were dried and weighed to obtain plant dry biomass (top + bottom). To estimate seed production, the seeds were isolated from the dried plant materials, stored in paper envelopes and weighed. All materials were dried in an oven at 50°C for at least 14 days and weighed using a digital scale.</p> <p>Variables names and meaning:</p> <p>PlantID: Individual identifier for each plant<br> nb_seeds_estimate.TOP: Number of seeds form the top section of the plant <br> Biomass.BOTTOM: Dry biomass of the bottom plant section (grams) <br> Total_biomass: Dry biomass of the whole aboveground plant materials, except for the male flowers <br> Biomass.TOP: Dry biomass of the bottom plant section (grams) <br> seed_mass_total: Dry biomass of the seeds of the whole plant (top+bottom sections) (grams)<br> seed_mass.BOTTOM: Dry biomass of the seeds from the bottom section (grams)<br> seed_nb_total: Number of seeds from the whole plant (top+bottom sections) <br> Lenght_section.TOP: Length of the top section (cm) <br> Fruit_number.TOP: Number of fruits present on the top sectioon at the time of harvest<br> nb_seeds_estimate.BOTTOM: Number of seeds from the bottom section<br> Height: Plant height (top+bottom sections) (cm) at the time of harvest<br> Fruit_number.BOTTOM: Number of fruits present on the bottom section at the time of harvest <br> DPT: Days-post-treatment = the period elapsed between the last treatment application and the plant sampling date. For logistical reasons, our sampling was spread over 14 days by a team of six assistants.<br> Lenght_section.BOTTOM: Length of the bottom section (cm)<br> Treatment: Herbivory treatments: C=Control; H= 25% chronic tissue loss, JA=exogenous jasmonate application; JAH=tissue loss + jasmonate.<br> Box: Enclosure in which plants were kept. This was a blocking factor with 2 boxes per treatment, each one with 30-32 plants. <br> Date: sampling date <br> seed_mass.TOP: Dry biomass of the seeds on the bottom plant sections (grams)<br> Observer: Identifier for each of the six researchers who sampled plants. We recorder observer identity and included it in our statistical analyses to account for possible biases among assistants.<br> male_fl_mass.TOP: Dry biomass of the male flowers sampled from the top plant section (grams). <br> nb_fl_estimate.TOP: Number of male flowers present on the top plant section at the time of harvest <br> male_fl_mass.BOTTOM: Dry biomass of the male flowers sampled from the bottom plant section (grams). <br> nb_fl_estimate.BOTTOM: Number of male flowers present on the bottom plant section at the time of harvest </p> <p> </p>
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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.