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Dataset results
29 results for “1000 Genomes”
1000 Genomes Data: Sequencing Data in BAM Format - LPA Region
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Denovo SPAdes assemblies for isolates included in the 1000-genome panel of Zymoseptoria tritici
<p>SPAdes draft assemblies for isolates included in the 1000-genome panel of <em>Zymoseptoria tritici</em></p> <p> </p> <p>For methods, please refer to: <a href="https://doi.org/10.1038/s41467-023-36674-y"><span>https://doi.org/10.1038/s41467-023-36674-y</span></a></p> <div> <div> </div> </div> <p>Original abstract: </p> <div> <div> <p>Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of <em>Zymoseptoria tritici</em>, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.</p> </div> </div>
European LD scores from 1000 Genomes
<p>This is a gzipped copy of the European LD scores from 1000 Genomes provided by the Alkes Group, originally available at https://data.broadinstitute.org/alkesgroup/LDSCORE/eur_w_ld_chr.tar.bz2.</p>
Data from: Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data
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Geographic allele frequency variation in the 1000 Genomes hg38 NYGC dataset
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spVCF for the resequenced 1000 Genomes Project (chr21)
<p>chr21 <a href="https://github.com/mlin/spVCF">spvcf.gz</a> file derived from <a href="https://www.internationalgenome.org/data-portal/data-collection/30x-grch38">New York Genome Center's GATK joint variant call set</a> of <a href="https://www.nature.com/articles/nature15393">1000 Genomes Project</a> whole-genome resequencing (N=2,504), roughly 1/5 of the original vcf.gz file size.</p> <p> </p> <p> </p>
1000 Genomes (Phase 3, GRCh37 -- split into five superpopulations)
<p>Genotype data for individuals from the 1000 Genomes project, split by superpopulation. Simple summary statistics are pre-computed and provided. Each superpopulation consists of a <strong>.bed</strong>, <strong>.bim</strong> and <strong>.fam</strong> file. The original 1000 Genomes dataset is available on the website (https://www.internationalgenome.org/), but the download page itself can be difficult to navigate. Thus, this data serves a straightforward access point to the data.</p> <p>One population, Yorubans (YRI), a subset of individuals from the African (AFR) superpopulation, is also included. Other subsets of individuals can be obtained by running PLINK2 commands on the superpopulation data.</p> <p>Data is used in (1) analysis of independence of LD blocks; (2) performing fine-mapping against GEUVADIS gene expression phenotypes. </p>
RNA-seq from four balanced translocation carriers in 1000 Genomes Project
GEO Series GSE94043. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
1000 Genomes Phase 3 aCGH samples
GEO Series GSE70188. Homo sapiens. 2534 samples. Type: Genome variation profiling by genome tiling array.
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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)
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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.