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549 results for “SNP data”
Data for "How Array Design Creates SNP Ascertainement Bias"
<p>The repository contains the raw SNP data in vcf format for the publication "How Array Design Creates SNP Ascertainment Bias". Note that the variants are <strong>not</strong> filtered at this timepoint. Samples starting with pl_ are pooled sequences of ~10 individuals while samples starting with i_ were individually sequenced. Please find detailed information about samples, raw sequencing data and SNP calling pipeline in the linked preprint (<a href="https://doi.org/10.1101/833541">https://doi.org/10.1101/833541</a>)/ publication (<a href="https://doi.org/10.1371/journal.pone.0245178">https://doi.org/10.1371/journal.pone.0245178</a>). In case you need additional information, please contact<a href="mailto:johannes.geibel@uni-goettingen.de"> johannes.geibel@uni-goettingen.de</a></p>
SNP and indel discovery and genotyping in next-generation sequencing data
<p>Code, logs and data for discovery and genotyping of SNPs and indels, in the the D.melanogaster genome, using GATK HaplotypeCaller. Code is in the zipped folder named code.zip. Run logs for this code as in the zipped folder named logs.zip. The unfiltered vcf genotypes file is named lhm_rg_HC_2015-09-15.vcf.gz. The filtered vcf genotypes file is named f1.lhm_rg_HC_raw.vcf.gz. The vcf submitted to NCBI dbSNP (filtered, and with indels >50bp and variants with null alternate alleles both removed) is named dbSNP.lhm_rg_HC_raw.vcf.gz. The folder local_reference.zip contains the reference assembly files against which genotypes were called against, and includes the code used to format the data prior to use. Also included is genotypes data from the two in-house reference line samples sequenced (BDGP6+ISO1 mito/dm6, Bloomington <em>Drosophila</em> Stock Center no. 2057)</p> <p>Samples are 220 Sussex-LH<sub>M</sub> hemiclones, and 2 RG. The first run did not include chromosome 4 and the mitochondrial genome, so these were genotyped separately, and then added to the rest of the results.</p> <p>The link for the NCBI dbSNP record is currently https://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewBatch.cgi?sbid=1062461and the submitter handle is MORROW_EBE_SUSSEX.</p> <p>At the time of writting, the NCBI D.melanogaster build is still being updated, and therefore ss identifiers, but not rs identifers are available.</p> <p>The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p>
Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams
<p>DNA were derived from fin tissue samples taken from individual trout captured from Little Jacks Creek, Big Jacks Creek , and Duncan Creek of the Owyhee mountains and Keithly Creek and Upper Mann Creek in the Hitt mountains of Western Idaho, United States. Fin tissues were collected from individual trout from each stream during monthly sampling events in June through October 2020. </p> <p><em>DNA Extraction:</em> Extraction of DNA from caudal fin tissues were performed using Quick-DNA Miniprep Plus purification kits (Zymo Research Inc.©). Small sections of fin tissue (≤ 25 mg) were collected from each sample. This was mixed with a digesting solution comprised of ultra-pure water, solid tissue buffer (Zymo Research Inc.©) and proteinase K. All tissues were digested in sealed microcentrifuge tubes for at minimum 3 h at 55°C in a water bath. We then aliquoted 100 µL of digestion supernatant and combined with 200 µL of genomic binding buffer (Zymo Research Inc.©). DNA was eluted in 50, 75, and 100 µL of elution buffer to determine which volume provided sufficient DNA concentration for genotyping. After it was determined all quantities produced suitable concentrations, going forward, 50 µL of elution buffer used.</p> <p><em>Genotyping:</em> Following extraction, genotyping-in-thousands sequencing took place at the Hagerman National Fish Hatchery’s genetics research facility with the assistance of the Columbia River Intertribal Fish Commission (CRTFC). Genotyping protocols were as described in Campbell et al. (2015) and summarized below. First, samples were prepared for amplification via PCR by combining DNA extracts with a Qiagen Plus multiplex master mix and a species-specific pooled primer mix. This step added the Illumina sequencing primer sites to amplicons. Following the creation of the PCR cocktail, thermocycling was conducted for amplification. Amplified samples were then diluted 20-fold. Diluted samples were transferred to new 96-well PCR plates where two genetic indexes and barcodes provides a unique set of tagging primers to each well and plate. Tagged plates then underwent a second PCR step. After the second PCR, all DNA were transferred to Charm Biotech normalization plates where DNA was bound to wells, washed, and finally eluted. After normalization, all DNA was pooled together and a purification step using magnetized beads in two steps to selectively remove fragments of DNA that are both too large and too small for sequencing. Following purification, each plate was quantified via qPCR using Life Technologies QuantStudio 6 Flex Instrument (Life Technologies). Finally, sequencing was performed using an Illumina HiSeq 1500 instrument.</p> <p><strong>Ancillary peer-reviewed manuscripts:</strong><br> <em>Genotyping protocols</em><br> Campbell NR, Harmon SA, Narum SR. 2015. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour, 15: 855-867. https://doi.org/10.1111/1755-0998.12357<br> <em>SNP loci reference</em><br> Collins EE, Hargrove JS, Delomas TA, Narum SR. 2020. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecology and Evolution, 10(17): 9486-9502. https://doi.org/10.1002/ece3.6641 </p> <p><strong>Data Use</strong>:<br> <em>License</em>: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> <br> <em>Recommended Citation</em>: Wooding AP, Narum SR, Pradhan DS. 2022. Data from: Development of Single Nucleotide Polymorphism (SNP) Panel for determination of environmental influence on genome for wild Columbia River redband trout (Oncorhynchus mykiss gairdnerii) in Southwest Idaho streams (0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7055582</p> <p>Funding for this project is provided by US National Science Foundation and Idaho EPSCoR through award: OIA-1757324 </p>
Planform change and Fundulus SNP data for small watersheds in South Mississippi and Louisiana
<p>Fluvial geomorphic processes and the resulting patterns of landform morphogenesis affect the distribution and connectivity of habitat patches for aquatic organisms. Human alterations to fluvial geomorphic processes may affect local habitat quality and stability, and affect connectivity of habitat patches by altering the distribution, supply, and movement of landform-generating materials. This dataset examines 17 watersheds in south Mississippi and southeastern Louisiana and was used in preparation of a manuscript addressing the hypothesis that elevated planform movement, indicative of advanced fluvial erosion, would cause fragmentation among populations of a headwater specialist (Blackspotted Topminnow <em>Fundulus olivaceus</em>). The dataset includes numerous spatial features derived from the NHD+ dataset used in planform measurements, spatial features digitized from NAPP and NAIP aerial imagery measuring planform characteristics and dynamics, additional metrics of each watershed, and a population genetics dataset of single nucleotide polymorphisms (SNPs) for multiple individuals at multiple sites per watershed. Associated code to recreate all analyses in the manuscript is provided.</p>
70K SNP array data for Lumpfish (Cyclopterus lumpus) across the trans-Atlantic
<p>In marine species with large populations and high dispersal potential, large-scale genetic differences and clinal trends in allele frequency can provide insight into the evolutionary processes that shape diversity. Lumpfish, <em>Cyclopterus lumpus</em>, is found throughout the North Atlantic and has traditionally been harvested for roe and more recently used as a cleaner fish in salmon aquaculture. We used a 70K SNP array to evaluate trans-Atlantic differentiation, genetic structuring, and clinal variation across the North Atlantic. Basin-scale structuring between the Northeast and Northwest Atlantic was significant, with enrichment for loci associated with developmental/mitochondrial function. We identified a putative structural variant on chromosome 2, likely contributing to differentiation between Northeast and Northwest Atlantic Lumpfish, and consistent with post-glacial trans-Atlantic secondary contact. Redundancy Analysis identified climate associations both in the Northeast (<em>N</em> = 1269 loci) and Northwest (<em>N</em> = 1637 loci), with 103 shared loci between them. Clinal patterns in allele frequencies were observed in some loci (15% - Northwest and 5% - Northeast) of which 708 loci were shared and involved with growth, developmental processes, and locomotion. The combined evidence of trans-Atlantic differentiation, environmental associations, and clinal loci, suggests that both regional and large-scale potentially-adaptive population structuring is present across the North Atlantic.</p>
SNP call data for: The current epidemic of the barley pathogen Ramularia collo-cygni derives from a recent population expansion and shows global admixture
<p>Ramularia Leaf Spot is becoming an ever increasing problem in main barley growing regions since the 1980s, causing up to 70% yield loss in extreme cases. Yet, the causal agent <em>Ramularia collo-cygni</em>, remains poorly studied. The diversity of the pathogen in the field thus far remains unknown. Furthermore, it is unknown to which extend the pathogen has a sexual reproductive cycle. To date, the teleomorph of <em>R. collo-cygni</em> has not been observed.</p> <p>To study the genetic diversity of <em>R. collo-cygni </em>and to get more insights into its biology, we sequenced the genomes of 19 <em>R. collo-cygn</em>i isolates from multiple geographic locations and diverse hosts. Here we share the SNP call data as well as the reference genome.</p> <p>The reference genome files and assembly can be found on ENI: GCA_900074925.1</p> <p>https://www.ebi.ac.uk/ena/data/view/GCA_900074925.1</p> <p>The raw sequence data is also available through ENI: ERX2296228</p> <p>https://www.ebi.ac.uk/ena/data/view/ERX2296228</p>
SNP data for the SwAsp collection
<p>DNP data for 94 individuals from the SwAsp collection, described in Luquez et al. (2008). Details about sequencing and SNP calling can be found in Wang et al. (2018). Data is mapped agains the <em>P. tremula </em>genome assembly v1.1(Lin et al. 2018).</p> <p><strong>References</strong></p> <p><strong><strong><strong>Lin Y-C</strong>, <strong>Wang J</strong>, <strong>Delhomme N</strong>, <strong>Schiffthaler B</strong>, <strong>Sundström G</strong>, <strong>Zuccolo A</strong>, <strong>Nystedt B</strong>, <strong>Hvidsten TR</strong>, <strong>de la Torre A</strong>, <strong>Cossu RM</strong>, <em>et al.</em></strong></strong> <strong>2018</strong>. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. <em>Proceedings of the National Academy of Sciences of the United States of America</em> <strong>115</strong>: E10970–E10978.</p> <p><strong><strong>Luquez V</strong>, <strong>Hall D</strong>, <strong>Albrectsen BR</strong>, <strong>Karlsson J</strong>, <strong>Ingvarsson P</strong>, <strong>Jansson S</strong></strong>. <strong>2008</strong>. Natural phenological variation in aspen (<em>Populus tremula</em>): the SwAsp collection. <em>Tree Genetics & Genomes</em> <strong>4</strong>: 279–292.</p> <p><strong><strong><strong>Wang J</strong>, <strong>Ding J</strong>, <strong>Tan B</strong>, <strong>Robinson KM</strong>, <strong>Michelson IH</strong>, <strong>Johansson A</strong>, <strong>Nystedt B</strong>, <strong>Scofield DG</strong>, <strong>Nilsson O</strong>, <strong>Jansson S</strong>, <em>et al.</em></strong></strong> <strong>2018</strong>. A major locus controls local adaptation and adaptive life history variation in a perennial plant. <em>Genome Biology</em> <strong>19</strong>: 72.</p>
SNP Data for Aedes aegypti populations in Florida and southern California
<p>In the affiliated paper we compare likely the oldest populations of <i>Aedes aegypti</i> in continental North America with some of the newest to illuminate the range of genetic diversity and structure that can be found within the invasive range of this important disease vector. <i>Aedes aegypti</i> populations in Florida have likely persisted since the 1600-1700s, while populations in southern California derive from new invasions that occurred in the last ten years. For this comparison, we genotyped 1,193 individuals from 29 sites at 12 highly variable microsatellites and a subset of these individuals at 23,961 single nucleotide polymorphisms (SNPs). This dataset contains the SNP genetic information.</p>
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
SNP Data for Aedes aegypti populations in Florida and southern California
Open the record for dataset details and reuse information.
70K SNP array data for Lumpfish (Cyclopterus lumpus) across the trans-Atlantic
Open the record for dataset details and reuse information.
Planform change and Fundulus SNP data for small watersheds in South Mississippi and Louisiana
Open the record for dataset details and reuse information.
Data from: Candidate gene SNP variation in floodplain populations of pedunculate oak (Quercus robur L.) near the species' southern range margin: weak differentiation yet distinct associations with water availability
<p>Populations residing near species' low-latitude range margins (LLM) often occur in warmer and drier environments than those in the core range. Thus, their genetic composition could be shaped by climatic drivers that differ from those occurring at higher latitudes, resulting in potentially adaptive variants of conservation value. Such variants could facilitate the adaptation of populations from other portions of the geographic range to similar future conditions anticipated under ongoing climate change. However, very few studies have assessed standing genetic variation at potentially adaptive loci in natural LLM populations. We investigated standing genetic variation at SNPs located within 117 candidate genes and its links to putative climatic selection pressures across 19 pedunculate oak (Quercus robur L.) populations distributed along a regional climatic gradient near the species' southern range margin in southeastern Europe. These populations are restricted to floodplain forests along large lowland rivers, whose hydric regime is undergoing significant shifts under modern rapid climate change. The populations showed very weak geographic structure, suggesting extensive genetic connectivity and gene flow or shared ancestry. We identified eight (6.2%) positive FST-outlier loci, and genotype-environment association analyses revealed consistent associations between SNP allele frequencies and several climatic variables linked to water availability. A total of 61 associations involving 37 SNPs (28.5%) from 35 annotated genes provided important insights into putative functional mechanisms in our system. Our findings provide empirical support for the role of LLM populations as sources of potentially adaptive variation that could enhance species' resilience to climate change-related pressures.</p>
Color scores, COI haplotypes and SNP data for Phelotrupes auratus individuals
<p>We studied the population genetic structure underlying the geographic variation in the structural color of the geotrupid dung beetle, <i>Phelotrupes auratus</i>,<i> </i>which exhibits metallic body colors of different reflectance wavelengths perceived as red, green, and indigo. These forms occur parapatrically in an area of Japan. The color variation was not related to variation in climatic factors. Using single-nucleotide polymorphisms (SNPs) from restriction-site associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red, and east/red) by a combination of genetic clusters (west, south, and east) and three color forms. There were three transition zones for the color forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colors. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident color changes, which implies regionally specific selection on the different colors. In a genome-wide association study, we identified four SNPs that were associated with the red/green or indigo color and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different color range. These loci may have controlled the transitions between different combinations of colors. Our study demonstrates that geographic color variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colors, and the effects of different color loci.</p>
Feline 60K SNP chip data originated from the domestic cat in Japan
<p>Pedigreed cats have traditionally been mated with close relatives, which increases the risks for inbreeding depression and genetic disorders. We evaluated the genome-wide population structure and the degree of inbreeding of 1022 cats, including 13 pedigreed and two random bred populations from Japan and the USA, using single nucleotide polymorphism array-based data. </p>
Data from: Phylogenetic relationships, breeding implications, and cultivation history of Hawaiian taro (Colocasia esculenta) through genome-wide SNP genotyping
Taro, Colocasia esculenta, is one of the world's oldest root crops and of particular economic and cultural significance in Hawai'i, where historically more than 150 different landraces were grown. We developed a genome-wide set of more than 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South Pacific, Palauan, and mainland Asian origins, with several objectives: (a) uncover the phylogenetic relationships between Hawaiian and other Pacific landraces, (b) shed light on the history of taro cultivation in Hawai'i, and (c) develop a tool to discriminate among Hawaiian and other taros. We found that almost all existing Hawaiian landraces fall into five monophyletic groups that are largely consistent with the traditional Hawaiian classification based on morphological characters, e.g., leaf shape and petiole color. Genetic diversity was low within these clades but considerably higher between them. Population structure analyses further indicated that the diversification of taro in Hawai'i most likely occurred by a combination of frequent somatic mutation and occasional hybridization. Unexpectedly, the South Pacific accessions were found nested within the clades mainly composed of Hawaiian accessions, rather than paraphyletic to them. This suggests that the origin of clades identified here preceded the colonization of Hawai'i, and that early Polynesian settlers brought taro landraces from different clades with them. In the absence of a sequenced genome, this marker set provides a valuable resource towards obtaining a genetic linkage map, and to study the genetic basis of phenotypic traits of interest to taro breeding such as disease resistance.
Data from: Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S attenuata) dolphins, from SNP data
Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin (Stenella longirostris) and the pantropical spotted dolphin (Stenella attenuata), using >3,000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species. Bayesian phylogeographic analyses of spinner dolphins showed deep divergence between Indo-Pacific, Atlantic, and eastern tropical Pacific Ocean (ETP) lineages. Despite high morphological variation, our results show very close relationships between endemic ETP spinner subspecies in relation to global diversity. The dwarf spinner dolphin is a monophyletic subspecies nested within a major clade of pantropical spinner dolphins from the Indian and western Pacific Ocean populations. Population-level division among the dwarf spinner dolphins was detected–with the northern Australia population being very different from that in Indonesia. In contrast to spinner dolphins, the major boundary for spotted dolphins is between offshore and coastal habitats in the ETP, supporting the current subspecies-level taxonomy. Comparing these species underscores the different scale at which population structure can arise, even in species that are similar in habitat (i.e., pelagic) and distribution.
SNP data for Northern Alligator Lizards
<p>Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (<em>Elgaria coerulea</em>), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single nucleotide polymorphism (SNP) data from 120 samples of <em>E. coerulea</em>. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for <em>E. coerulea</em>, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least ten distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in <em>E. coerulea</em> is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in <em>E. coerulea</em> are consistent with predictions from co-distributed species.</p>
Mingrelian SNP Genotype Data
<p>This dataset contains data from 645,337 single nucleotide polymorphisms (SNPs) that were genotyped on GenoChip 2+ microarrays. The SNP data were ascertained from the mtDNA, Y-chromosome and autosomes for each individual, depending on their biological sex. In total, 5,205 mtDNA and 10,272 Y-chromosome SNPs were extracted from the array data. These data files have been uploaded as .csv files and also be uploaded as plink-formatted files. Details about the analysis of the SNP data can be found in the associated manuscript:</p><p>Theodore G Schurr, Ramaz Shengelia, Michel Shamoon-Pour, David Chitanava, Shorena Laliashvili, Irma Laliashvili, Redate Kibret, Yanu Kume-Kangkolo, Irakli Akhvlediani, Lia Bitadze, Iain Mathieson, Aram Yardumian, Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus), <i>Genome Biology and Evolution</i>, 2023; evad198, <a href="https://doi.org/10.1093/gbe/evad198">https://doi.org/10.1093/gbe/evad198</a></p>
SNP data for F2 population derived from Oryza rufipogon and O. nivara
<p>To elucidate the genetic architecture underlying phenotypic divergence is essential to the understanding of ecological adaptation and speciation. Two wild rice species (<em>O. rufipogon</em> and <em>O. nivara</em>) are a progenitor-daughter species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolved linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F<sub>2</sub> population generated from a cross between the perennial <em>O. rufipogon</em> and annual <em>O. nivara</em>. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots), with each involving multiple adaptive traits, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and <em>v</em>-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits.</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)
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DANDI Archive for NWB datasets
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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.