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4,120 results for “sex”
Mink fecal microbiomes are influenced by sex, temperature and time post-defecation
<p>Mink metadata, QIIME2 artifacts and demultiplexed EMP-paired end sequences from Argonne National laboratory, R code for statistical analyses and figure generation, and QIIME2 pipeline for Lafferty et al. 2021.</p>
Male biased sex ratio in the offspring of roe deer
<p>The file "metafor_roe_sex.csv" was used for the meta-analysis regarding the sex ratio of roe deer juveniles. It contains the columns: </p> <p>Author (author(s) of the publication, Country (country were the study was publised), Location (specific location, in case that the data set contains several different locations the term "divers" is used), Year (year(s) were the sex of roe deer offspring were documented), Pub-Year (Year of publication) , N (number of offspring), N_female (number of female offspring), Sex ratio (primary - P or secondary - S sex ratio), Habitat conditions (F - free ranging, I - Island conditions, C - captive), Proportion female (proportion of female juveniles), Low_95 (lower boundary for the proportion of females using an exact binomial test with a 95% confidence interval), High_95 (upper boundary for the proportion of females using an exact binomial test with a 95% confidence interval), d (effect size), d_se (standard error of the effect size), North (Latitude), East (Longitude)</p> <p>The file "sex_bw.csv" contains information about roe deer juveniles tacked in Baden-Württemberg. The columns read as: Year (year were the juvenile was tacked), sex (the sex of the juvenile, m- male; f- female), and Hasl (elevation in m)</p> <p>The file "temp_data_comma_sep.csv" contains the montly mean values for temperature (Temp) and precipitation (NDS) for the months January, February, March, ..., December for the German federal state Baden-Württemberg (Source German Weather Service).</p> <p>All data sets were used for analysis presented in: Evidence for a male-biased sex ratio in the offspring of a large herbivore: the role of environmental conditions in the sex ratio variation.</p> <p> </p> <p> </p>
Data and code for: Insect herbivores drive sex allocation in angiosperm flowers
<p><strong>Code and Data for the paper:</strong></p> <p>Insect herbivores drive sex allocation in angiosperm flowers</p> <p><em>Carlos Roberto Fonseca, Martin M. Gossner, Johannes Kollmann, Martin Brändle, Gustavo Brant Paterno</em></p> <p> </p> <p>Content of the repository</p> <ol> <li> <p><strong>Data</strong>: the folder <code>data</code> contains all data required to reproduce analyses, figures and tables.</p> </li> <li> <p><strong>Outputs</strong>: the folder <code>output</code> contains the figures, tables and temporary files generated.</p> </li> <li> <p><strong>Code</strong>: the folder <code>scripts</code> contains all scripts (.R) that generated results, figures and tables used in the manuscript and in the supporting information.</p> </li> <li> <p><strong>Supplementary information</strong>: the folder <code>doc</code> contains the supplementary information associated to the paper.</p> </li> </ol>
Separate-sex GWAS for reproductive fitness in Drosophila melanogaster (Sussex LHM sample)
<p>Code, data, logs, and graphs for GWAS on seperate-sex reproductive fitness in Drosophila melanogaster, Sussex LHM population sample.</p> <p>The shell script, code_drive_basic_gwas.sh, downloads input data files from the internet, drives Plink to select LD-independent SNPs, and then perform a genome-wide association test against female and male fitness, separately. Plink is also used to assign functions and gene names to SNPs. Bash/Unix code is used for formatting/compatibility adjustments, and also to add NCBI-dbSNP IDs to results. The shell script starts an R script that generates basic diagnostic graphs. This updated version differs from the first in that three large unconfirmed snRNA genes have been omitted to improve assignment of SNPs to genes.</p> <p>See https://f1000research.com/articles/5-2644/v3 and http://www.sussex.ac.uk/lifesci/morrowlab/</p>
Dataset: Sex differences in the impact of social relationships on individual vocal signatures in grey mouse lemurs
<p>Dataset used in the statistical analysis of the publication "Sex differences in the impact of social relationships on individual vocal signatures in grey mouse lemurs (<em>Microcebus murinus</em>)"</p> <p><strong>Abstract</strong></p> <p>Vocali<span>z</span>ations coordinate social interactions between conspecifics by conveying information concerning the individual or group identity of the sender. Social accommodation is a form of vocal learning where social affinity is signalled by converging or diverging vocali<span>z</span>ations to those of conspecifics. To investigate whether social accommodation is linked to the social lifestyle of the sender, we investigated sex-specific differences in social accommodation in a dispersed living primate, the grey mouse lemur, where females form stable sleeping groups whereas males live solitarily. We used 482 trill calls of 36 individuals from our captive breeding colony to compare acoustic dissimilarity between individuals with genetic relatedness, social contact time and body weight. Our results showed that female trills become more similar the more time females spen<span>d</span> with each other independent of genetic relationship, suggesting vocal convergence. In contrast, male trills were affected more by genetic than social factors. However, focus<span>s</span>ing only on sociali<span>z</span>ed males, male trills diverged from each other the more time males were cage partners. Thus, grey mouse lemurs show the capacity for social accommodation, with females converging their trills to signal social closeness to sleeping group partners, whereas males do not adapt or diverge their trills to signal individual distinctiveness. </p> <p> </p> <p>For details concerning the recording of the trills confer to the publication at doi: 10.1098/rstb.2023.0193</p>
Images of article "Sexy ways: the methodical approaches to study plant sex chromosomes"
<p><strong>Figure 1. </strong>Schematic diagram of sex chromosome evolution in dioecious plants. Species are shown according to their level of sex chromosome differentiation and Y chromosome asynapsis. In<em> S. oleracea, A. officinalis</em> and <em>C. papaya</em>, the sex chromosomes are mostly homomorphic with recently formed non-recombining regions (region with suppressed recombination). The non recombining region is largely extended almost to entire chromosomal length in species with heteromorphic sex chromosomes, namely in <em>S. latifolia, R. hastatulus</em> (XY cytotype), <em>R. acetosa, H. lupulus, H. japonicus </em>and<em> M. polymorpha</em>. The position of the centromere, the PAR length and the ratio between X and Y is illustrative. </p> <p><strong>Figure 2.</strong> Laser microdissection as a tool to reduce genome complexity. Sex chromosomes in metaphase are isolated from plant cells (mostly pollen mother cells or root tips) and subsequently spread on a special microscopic slide covered with the membrane. After microdissection, chromosomes are transferred into a tube and processed to other applications. In case of chromosome sorting, the chromosome suspension is stained with a DNA-specific dye and introduced into a flow chamber. Within this chamber, individual chromosomes interact with a laser beam, and the scattered light and emitted fluorescence are measured. Through this process, a histogram of fluorescence intensity (known as a flow karyotype) is generated. Sorting is accomplished by breaking the liquid stream into droplets and electrically charging the droplets containing the chromosomes of interest.</p> <p><strong>Figure 3.</strong> Cytogenetic tools to study sex chromosome origin and evolution. Cytogenetics nowadays combine genomic tools to study repeat fraction including TEs and satellites (a), design unique barcodes to distinguish particular chromosome or chromosomal domain using chromosome oligo-painting probe design (b), and bioinformatic tools to dissect single chromosomes or genome parts (c). The combination of above methods helps to understand sex chromosome evolution regarding their autosomal origin, chromosomal rearrangements, and Y(W) chromosome differentiation. Arrows represent evolutionary steps during sex chromosome divergence (d). The sex chromosome barcoding allows understanding of meiotic pairing which in turn supports chromosomal fusions and inversion/translocations. To chromosomes belong to species with references, from the top to the bottom as follows: <em>S. latifolia </em>Ogre retroelement (Kubat et al., 2014), <em>R. hastatulus</em> XY cytotype satellite Cl135 (Sacchi et al., 2023, Preprint), <em>S. latifolia</em> PAR oligo-painting probe with the subtelomeric satellite X43.1 and centromeric satellite STAR-C (Bačovský et al., 2020), and the same DNA probes on chromosomes in metaphase I in <em>S. latifolia </em>(Bernasconi et al., 2009; Bačovský et al., 2022). </p> <p><strong>Figure 4.</strong> Methodical strategies to assess the function of sex chromosomes in plants. Experimental assays with polyploids (alternatively aneuploids) represent the classical way to determine the role of individual sex chromosomes (a). These assays with plants of various ploidy levels were usually supported by analyses of deletion lines (plants carrying short-chromosomal <br>deletions or microdeletions) (b) that allowed researchers to identify sex-linked regions involved in sex determination and floral development. Modern assays using reverse genetics, such as CRISPR/Cas9, virus-induced gene silencing (VIGS) or peptide treatment of shoot apical meristem (c) provide direct evidence of the gene function and its contribution to the development <br>of reproductive organs. Parasite infected (d) or chemically induced (e) hermaphrodites from either female or male individuals, e.g. in <em>Silene</em> or kaki, let to the identification of key mechanisms and genes that regulate sexual phenotypes, and to understand the regulatory networks leading to separate sexes. </p>
A comprehensive catalog of exact short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of exact repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,233,959 TR intervals, covering 0.783306% (24.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
Multi-study reanalysis of 2213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures
<p>Supplemental Information, Supplementary Tables, and Supplementary Files, as well as accompanying data for the manuscript "Stratified computational meta-analysis of 2213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures" by Raeuf Roushangar and George I. Mias. </p>
Data on the sex and age composition of Bramblings Fringilla montifringilla during autumn migration and winter in Europe
<p><strong>Abstract</strong></p> <p>Bramblings <em>Fringilla montifringilla</em> are known to vary in winter distribution according to sex and age (differential migration). This pattern is complicated by the large yearly fluctuation in their preferred winter food, beech seeds. In beechmast areas, large concentrations of Bramblings occur, and their sex and age composition differs from that of winters without a beechmast. Here we present data on the sex and age composition of Bramblings during autumn migration and winters with and without beechmast, mainly from Switzerland, supplemented with data from northern and southern Europe.</p> <p> </p> <p><strong>Literature cited in the Excel-file</strong></p> <p>Arizaga J, Zuberogoitia I, Zabala J, Crespo A, Iraeta A, Belamendia G (2012) Seasonal patterns of age and sex ratios, morphology and body mass of Bramblings <em>Fringilla montifringilla </em>at a large winter roost in southern Europe. Ring. Migr. 27:1–6. https://doi.org/10.1080/03078698.2012.686707</p> <p>Browne SJ, Mead CJ (2003) Age and sex composition, biometrics, site fidelity and origin of Brambling <em>Fringilla montifringilla </em>wintering in Norfolk, England. Ring. Migr. 21:145–153. https://doi.org/10.1080/03078698.2003.9674283</p> <p>Khil L, Samwald O, Tiefenbach A, Tiefenbach M, Pacher H (2011) Der Massenschlafplatz von Bergfinken <em>Fringilla montifringilla </em>in Österreich im Winter 2008/2009. Limicola 25:81–100</p> <p>Kjellén N, Lindström Å (1993) Bergfinkens övervintringsstrategier samt några iakttagelser från en skånsk sovplats i januari-februari 1993. Anser 32:187–199</p> <p>Robson D (1996) Influencia de la temperatura en la masa corporal del Pinzon Real. Ardeola 43:139–144</p> <p>Schierer A (1957) Geschlechts- und Altersverhältnis der Nordfinken. Vögel Heimat 27:68</p> <p>Widemo U (1977) Bergfink <em>Fringilla montifringilla </em>Jan. - Apr. 1977. Sex and age distribution, winglength and change of weight. Fåglar i Sörmland 10:76–81</p>
Dataset: Insular cortex dopamine 1 and 2 receptors in methamphetamine conditioned place preference and aversion: Age and sex differences
<p>Dataset for Insular cortex dopamine 1 and 2 receptors in methamphetamine conditioned place preference and aversion: Age and sex differences</p>
Protection from radiation-induced neuroanatomical deficits by CCL2-deficiency is dependent on sex
<p>This project investigated the impact of Ccl2 genotype status (+/+, +/-, -/-) on the brain structure changes induced by cranial radiation. Mn-enhanced MR images were acquired at P14, P23, P42, P63 and P98. Radiation (7-Gy) was delivered on P16 to the whole head, with a lead shield used to limit dose to the rest of the body. Further details are available in the manuscript.</p> <p>For the image processing, the registration was accomplished using the pydpiper toolkit (version 2.0.9), available on GitHub (https://github.com/Mouse-Imaging-Centre/pydpiper/tree/v2.0.9). A two-level registration was used. Key elements of that registration output are provided in this data posting.</p>
Data to support Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays"
<p>Datasets supporting the manuscript: Whitney JL, Coleman RR, Deakos MH "Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian Reef Manta Rays". <em>BMC Ecology and Evolution </em><strong>23</strong>, 31 (2023). https://doi.org/10.1186/s12862-023-02130-0</p> <p>Nuclear data:</p> <p>"Mobula-alfredi_nuclear_reference_RAD_contigs.fasta" is a fasta of 359,751 contigs that serve as the reference for nuclear alignment of genotypes to RAD loci. Contigs begin and end with GATC cut site.</p> <p>Mobula-alfredi_nuclear_all_2048snps_38genotypes.vcf is a VCF file with all 2048 nuclear SNPs in final filtered SNP dataset. 38 genotypes are included from Maui Nui and Hawaii Island. This 2048 SNPs includes both 2038 neutral and 10 outlier SNPs. </p> <p>Mobula-alfredi_nuclear_neutral_2038snps_38genotypes.vcf is a VCF file with 2038 neutral nuclear SNPs genotyped in 38 individuals from Maui Nui and Hawaii Island. </p> <p>Mobula-alfredi_nuclear_outliers_10snps_38genotypes.vcf is a VCF file with 10 outlier SNPs genotyped in 38 individuals from Maui Nui and Hawaii Island. </p> <p>Structure (.str) files are also provided in addition to VCFs. In all files Population prefixes M=Maui Nui and K=Hawaii Island. </p> <p>Mitochondrial data:</p> <p>Mobula-alfredi_mitogenome_34haplotypes_9sites_min4x.vcf is a VCF file with 9 variant sites across the mitogenome haplotyped in 34 individuals from Maui Nui and Hawaii Island. </p> <p>Mobula-alfredi_mitogenome_34haplotypes_allsites_min4x.fasta is a FASTA file with whole mitogenomes aligned to OP562409 [https://www.ncbi.nlm.nih.gov/nuccore/OP562409]. Sites with less than 4x coverage were masked with Ns. </p> <p>Mobula-alfredi_mitogenome_reference_OP562409.fasta is a FASTA file containing the <em>Mobula alfredi</em> reference mitogenome OP562409 [https://www.ncbi.nlm.nih.gov/nuccore/OP562409].</p> <p> </p>
Sex-specific changes in autosomal methylation rate in ageing common terns - Data
<p>In the manuscript "<strong>Sex-specific changes in autosomal methylation rate in aging common terns</strong>" published in Frontiers Ecology And Evolution, we investigate sex-specific age effects in global DNA methylation patterns in aging common terns in a longitudinal study. We collected blood at 1-, 3- and/or 4-year intervals, extracted DNA from the erythrocytes and estimated autosomal DNA methylation by mapping Reduced Representative Bisulfite Sequencing reads to a de novo assembled reference genome. </p> <p>The raw RRBS reads can be found at: https://www.ebi.ac.uk/ena, PRJEB48910 and the genome at https://www.ncbi.nlm.nih.gov/, PRJNA560234.</p> <p>This document contains the final data frame used for the GLMM. We further share a markdown document summarising the various scripts and programs used for the Reduced Representative Bisulfite Sequencing data analyses and GLMMs (e.g. RefFreeDMA, picard, bismark, and R) under another DOI: 10.5281/zenodo.7493357. </p>
Simulation code and simulated data for: Transient polymorphisms in parental care strategies drive divergence of sex roles
<p>This repository contains C++ code, simulated datasets, an R-script for data analysis and a Mathematica notebook for mathetical analysis.</p><p>Datasets are organised into ZIP files named after the corresponding figure in the publication. All of the figures based on simulation data in the manuscript and supplementary materials can be created with the R-script. For further information see the article published in <i>Nature Communications (</i>doi:<i> </i>https://doi.org/10.1038/s41467-023-42607-6).</p><p> </p><p> </p><p> </p>
Data from: Sex differences in the relationship between maternal and foetal glucocorticoids in a free-ranging large mammal
<p><strong>Description</strong><br> <br> This registration contains the data and scripts used for the analysis in the manuscript "Sex differences in the relationship between maternal and neonate cortisol in a free-ranging large mammal" (https://doi.org/10.1101/2023.05.04.538920). All versions and additional material are posted on the OSF project page: https://osf.io/4ymc8/ </p> <p>Important to note: this is an updated registration from a previous version (www.osf.io/wynke). OSF currently does not allow to change the files that were uploaded previously, which is why we switched to Zenodo. Future updates to the dataset and scripts will take place here. </p> <p><br> <strong>Changes to previous version</strong></p> <p>Following our review process at PCI Ecology, we made some changes (mostly additions) to the previous version. This includes the addition of more raw data. </p> <p>Changes to the previous version include: </p> <p>- We added the raw faecal data (“Raw_faecal_data.csv) along with a script (“Faecal exploration .R”), which loads the raw faecal datafile and does some minor investigations on it. These include checking whether the sampling time or day matter, and calculating a repeatability estimate.<br> - In “Faecal exploration.R”, we highlight the outlier that we removed. <br> - We have added the t-test reported in the manuscript to the script “Analysis.R”.<br> - In “Analysis.R”, we now also run the analysis both with as well as without the outlier. We also have adapted our code to plot the outlier in the figure along with the other values. <br> - We have updated the README file to include a description of both the data files and the scripts. <br> </p>
Connectomes, APOE, Age, Sex, and Diet in Mouse Models of Aging
<p>Brain networks and covariates for mouse models of aging. Includes APOE22/33/44 with and without HN, age, sex, and diet.</p> <p>Files:</p> <p>- connectomes.rda: a tensor of symmetric adjacency matrices corresponding to brain networks.</p> <p>- mice.rda: a dataframe containing mouse covariates.</p> <p>- mouse_anatomy.csv: a table containing scientific names for each brain region in connectomes.rda.</p>
Figures 1-8 in A description of the flea species Paractenopsyllus madagascarensis n. sp. and the female sex of Paractenopsyllus raxworthyi Duchemin & Ratovonjato, 2004 (Siphonaptera, Leptopsyllidae) from Madagascar with a key to the species of Paractenopsyllus
Figures 1-8. Paractenopsyllus madagascarensis sp. n. 1 Head and thorax, holotype 3 (SMG-13919). 2 Head and thorax, allotype ♀ (SMG-13903). 3 Aedeagus, paratype 3 (SMG-14002). 4 Apex of aedeagus, paratype 3 (SMG-14002). 5 Basimere and telomere, mesal aspect, paratype 3 (SMG-14002). 6 Eighth tergite, paratype 3, (SMG-14002). 7 Eighth sternite, paratype 3 (SMG-14002). 8 Ninth sternite, paratype 3 (SMG-14002). Scale = 200µ
Figure 14-16 in A description of the flea species Paractenopsyllus madagascarensis n. sp. and the female sex of Paractenopsyllus raxworthyi Duchemin & Ratovonjato, 2004 (Siphonaptera, Leptopsyllidae) from Madagascar with a key to the species of Paractenopsyllus
Figure 14-16. Paractenopsyllus raxworthyi, ♀ (MR-172). 14 Head and pronotum. 15 Seventh sternum and eighth tergum. 16 Spermatheca and bursa copulatrix. Scale 14-15 = 200µ, 16 = 100µ
Figure 9-13 in A description of the flea species Paractenopsyllus madagascarensis n. sp. and the female sex of Paractenopsyllus raxworthyi Duchemin & Ratovonjato, 2004 (Siphonaptera, Leptopsyllidae) from Madagascar with a key to the species of Paractenopsyllus
Figure 9-13. Paractenopsyllus madagascarensis sp. n. 9 Seventh sternite and terminalia, allotype ♀ (SMG- 13903). 10 Spermatheca and bursa copulatrix, allotype ♀ (SMG-13903). 11 Spermatheca and bursa copulatrix, paratype ♀ (SMG-13935). 12 Anal stylet, paratype ♀ (SMG-13918). 13 Hind tibia, holotype 3 (SMG-13919). Scale 9 and 13 = 200µ, 10-12 = 100µ
Raw data for: Sex and Power: Sexual dimorphism in trait variability and its eco-evolutionary and statistical implications
<p>This is a dataset obtained from the EBI in August 2018. The full code, analyses and processed data that are associated with the paper that is based on this large dataset can be found here: <a href="https://github.com/itchyshin/mice_sex_diff">https://github.com/itchyshin/mice_sex_diff</a></p> <p> </p>
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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.