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27 results for “Y-chromosome”
Y-chromosome and mitochondrial data for the article entitled: "The First Horse Herders and the Impact of Early Bronze Age Steppe Expansions into Asia"
<p>Y-chromosome and mitochondrial data for the article entitled: "The First Horse Herders and the Impact of Early Bronze Age Steppe Expansions into Asia"</p>
Frequency maps of Y-chromosomal haplogroups in Finland - out of all samples
<p>Y-chromosomal regional enrichment maps for all haplogroups with at least 1% frequency in Finland out of all samples. A star (*) within the map and gray color in the forest plot indicates the frequency is inferred by combining samples from geographically closest regions due to low coverage of samples in the region.</p>
Frequency maps of Y-chromosomal haplogroups in Finland - out of major haplogroup
<p>Y-chromosomal regional enrichment maps for all haplogroups with at least 1% frequency in Finland out of major haplogroup carriers (N1a1, I1a, R1a and R1b). A star (*) within the map and gray color in the forest plot indicates the frequency is inferred by combining samples from geographically closest regions due to low coverage of samples in the region.</p>
Y-SNP data for Y-chromosome genetic characterization of Tibetan antelope supporting conservation efforts
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Aneuploidies in Embryos and Spermatozoa From Patients With Y-chromosome Microdeletions
ClinicalTrials.gov study NCT02527954. IPD Sharing: Not stated. Countries: 1. Publications: 27.
Data from: Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes
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Data from: Y-chromosome markers for the red fox
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Data from: Y-chromosomes can constrain adaptive evolution via epistatic interactions with other chromosomes
Background: Variation in the non-coding regions of Y-chromosomes have been shown to influence gene regulation throughout the genome in some systems; a phenomenon termed Y-linked regulatory variation (YRV). This type of sex-specific genetic variance could have important implications for the evolution of male and female traits. If YRV contributes to the additive genetic variation of an autosomally coded trait shared between the sexes (e.g. body size), then selection could facilitate sexually dimorphic evolution via the Y-chromosome. In contrast, if YRV is entirely non-additive (i.e. interacts epistatically with other chromosomes), then Y-chromosomes could constrain trait evolution in both sexes whenever they are selected for the same trait value. The ability for this phenomenon to influence such fundamental evolutionary dynamics remains unexplored. Results: Here we address the evolutionary contribution of Y-linked variance by selecting for improved male geotaxis in populations possessing multiple Y-chromosomes (i.e. possessed Y-linked additive and/or epistatic variation) or a single Y-chromosome variant (i.e. possessed no Y-linked variation). We found that males from populations possessing Y-linked variation did not significantly respond to selection; however, males from populations with no Y-linked variation did respond. These patterns suggest the presence of a large quantity of Y-linked epistatic variance in the multi-Y population that dramatically slowed its response. Conclusions: Our results imply that YRV is unlikely to facilitate the evolution of sexually dimorphic traits (at least for the trait examined here), but can interfere with the rate of trait evolution in both males and females. This result could have real biological implications as it suggests that YRV can affect how quickly a population responds to new selective pressures (e.g. invasive species, novel pathogens, or climate change). Considering that YRV influences hundreds of genes and is likely typical of other independently-evolved hemizygous chromosomes, YRV-like phenomena may represent common and significant costs to hemizygous sex determination.
Data from: Y-chromosome structural diversity in the bonobo and chimpanzee lineages
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Data from: Y-chromosomes can constrain adaptive evolution via epistatic interactions with other chromosomes
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Genome-wide gene expression analysis of Y-chromosome aneuploidy strains of Drosophila melanogaster
GEO Series GSE93699. Drosophila melanogaster. 30 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide small RNAs expression analysis of Y-chromosome aneuploidy strains of Drosophila melanogaster
GEO Series GSE93700. Drosophila melanogaster. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Systematic identification of Y-chromosome gene functions in mouse spermatogenesis [10x]
GEO Series GSE274095. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Sheep Y-chromosome methylation profile from long reads sequencing data
GEO Series GSE262831. Ovis aries. 2 samples. Type: Methylation profiling by high throughput sequencing.
Systematic identification of Y-chromosome gene functions in mouse spermatogenesis [bulk]
GEO Series GSE274100. Mus musculus. 120 samples. Type: Expression profiling by high throughput sequencing.
Cattle Y-chromosome methylation profile from long reads sequencing data
GEO Series GSE263098. Bos taurus. 2 samples. Type: Other.
Analysis of testicular transcriptome changes in the presence of Y-chromosomal microdeletions
GEO Series GSE21613. Homo sapiens. 34 samples. Type: Expression profiling by array.
Genome-wide gene and small RNA expression analysis of Y-chromosome aneuploidy strains of Drosophila melanogaster
GEO Series GSE93701. Drosophila melanogaster. 42 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Supplementary data for human Y-chromosome gene expression analysis
<p>Processed data for:</p> <p>AK Godfrey, S Naqvi, L Chmátal, JM Chick, RN Mitchell, SP Gygi, H Skaletsky, DC Page. Quantitative analysis of Y-chromosome gene expression across 36 human tissues. <em>Genome Res</em> (2020).</p> <p>The following six files are provided for reference and for use in future analyses.</p> <p>(1) <strong>gencode.v24.annotation.basic_ccds_nopar.gtf.gz</strong> — transcriptome annotation used in analyses</p> <p>(2) <strong>gtex.ksto.gen24c.prefilt_pass1.genes.est_counts.txt.gz</strong> — genes x samples matrix containing estimated count values output by kallisto for all samples passing initial set of metadata-based filters.</p> <p>(3) <strong>gtex.ksto.gen24c.prefilt_pass1.pcgenes.tpm.txt.gz</strong> — protein-coding genes x samples matrix containing TPM values output by kallisto for all samples passing initial set of metadata-based filters. </p> <p>(4) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.tpm.txt.gz </strong>— protein-coding genes x samples matrix containing TPM values output by kallisto for samples passing initial metadata-based filters and expression-outlier filters.</p> <p>(5) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.adj_tpm.txt.gz </strong>— protein-coding genes x samples matrix (based on file #4 above) containing TPM values adjusted for RIN, ischemic time, and intronic-read mapping rate.</p> <p>(6) <strong>gtex_metadata_subset.txt</strong> — sample/donor metadata</p> <p>The remaining 24 files contain the input data required to replicate analyses in the manuscript, as detailed at <a href="https://github.com/akg8/MSY-expression">https://github.com/akg8/MSY-expression</a>. HDF5 (`.h5`) files contain individual <a href="https://pandas.pydata.org">pandas</a> DataFrame objects with the key `df`. These files can be downloaded individually, or they can be downloaded all at once by downloading the file <strong>msy_expression.all_input_data.zip </strong>(recommended).</p> <p>---</p> <p><strong>Version history:</strong></p> <ul> <li><strong>Version 1</strong> contained just the six listed files above.</li> <li>In <strong>Version 2</strong>, the remaining 24 files needed for reproducing analyses were added. In addition, gtex_metadata_subset.txt was updated with the previously missing column `SEX`.</li> <li>In <strong>Version 3</strong>, a single zipped file msy_expression.all_input_data.zip was added so that all input data for re-analysis can be downloaded more conveniently.</li> </ul>
Toxic Y-chromosome in D. miranda
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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.