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899 results for “allele”
Data from: Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)
Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.
Allele scores and frequencies of 66 microsatellite locus loci in Solenopsis invicta
<p>Allele scores and frequencies of 66 microsatellite loci in <em>Solenopsis invicta </em>samples were analyzed from 65 populations and 1,074 individuals.</p> <p>65 populations were collected from South Korea, China, Taiwan, and the United States.</p>
Late steps of allelic break-induced replication suppress tandem duplication associated with BRCA1 deficiency
<p><a name="OLE_LINK1"></a><span lang="EN-US">Microhomology-mediated tandem duplication (TD) is a distinct mutational signature in <em>BRCA1</em>-deficient tumors. While several mechanisms have been proposed for its generation, much understanding comes from repeat-based reporters, which may not represent the region of the human genome lacking neighboring repeats. To address this limitation, we developed a repeat-less TD reporter and a PCR-based endogenous site-specific TD assay to examine TDs induced by replication-coupled single-ended DNA double-strand breaks (seDSBs) in <em>Brca1</em>-deficient mouse embryonic stem cells. We found that TDs from seDSBs were detectable in normal cells but significantly increased in <em>Brca1</em>-deficient cells. This increase did not involve classical non-homologous end joining. TD formation appeared to be facilitated by a switch to microhomology-mediated non-allelic sister chromatid recombination from initial allelic DNA synthesis, suggesting that allelic DNA synthesis, a late step of allelic break-induced replication (aBIR), is more prone to premature termination in <em>Brca1</em>-deficient cells, promoting TDs. Disrupting RAD51 loading reduced TDs in wild-type cells but not in <em>Brca1</em>-deficient cells, indicating both RAD51-dependent and -independent pathways for TD formation. Additionally, RAD54 and BRCA1-BARD1 suppressed TDs in a RAD51-dependent manner, with BARD1's effect partially mediated through RAD51 interaction. These findings together implicate late steps of aBIR in TD suppression and provide novel insights into the mechanisms underlying <em>BRCA1</em>-linked TD formation in cancer.</span></p> <p><span lang="EN-US"> </span></p>
Genetic variability among and within domestic Old and New World Camels at the α-lactalbumin gene (LALBA) reveals new alleles and polymorphisms responsible for differential expression
<p><strong>Supplementary Figure 1</strong>. Schematic representation of the <em>LALBA</em> gene in camelids. Boxes indicate the exons (black for the un-translated, white for the signal peptide and grey for the translated). The line shows introns, 5’- and 3’-flanking regions.</p> <p><strong>Supplementary Figure 2</strong><strong>. </strong>Alignment of the α-LA calcium-binding site (red rectangle) of 23 terrestrial species available in the UniProt database (<a href="http://www.uniprot.org/uniprot/">http://www.uniprot.org/uniprot/</a>). The calcium-binding site in the <em>Camelus dromedarius</em> is indicated by a yellow rectangle.</p>
SNP alleles for pooled DNA samples of Vicia villosa targeting QTL for pod dehiscence and seed dormancy
<p>Hairy vetch (<em>Vicia villosa </em>Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy. We used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. We also combined pooled DNA sample genetic association results with the results of a prior genome-wide association study. Genomic prediction resulted in positive predictive abilities for both traits between environments and with an independent dataset (0.34-0.50), but reduced predictive ability for DNA pools with divergent seed dormancy in the Maryland environments (0.07-0.15). The pooled DNA samples found six significant (false discovery rate q-value<0.01) quantitative trait loci (QTL) for seed dormancy and four significant QTL for pod dehiscence. Unfortunately, the minor alleles of the pod dehiscence QTL increased the rate of pod dehiscence and are not useful for marker-assisted selection. When combined with a prior association study, sixteen seed dormancy QTL and zero pod dehiscence QTL were significant. Combining the association studies did not increase the detection of useful QTL.</p>
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics (output data)
<p>This contains the output results of CalicoST (inferred CNAs and cancer clones), results of comparison methods, and CNAs inferred from WES data of 13 samples across four cancer types.</p> <p>In this updated version, we also included the simulated data and the results from CalicoST and other methods in CalicoST_simulation_deposit.zip. README contains the details of deposited files.</p>
Kcnma1-tdtomato floxed allele sequence
<p>BK large conductance calcium-activated K+ channels (KCa1.1) are expressed widely across many tissues, contributing to systemic regulation of cardiovascular, neurological, and other specialized physiological functions. The pore-forming α subunit is encoded by the <em>Kcnma1</em> gene, originally named <em>mSlo1</em> in mouse and <em>slowpoke</em> in <em>Drosophila</em>. Global deletion in mouse (<em>Kcnma1−/−</em>) produces a plethora of defects in neuron and muscle excitability, as well as other phenotypes related to channel function in nonexcitable cells. While homozygous null mice are viable, the ubiquitous loss of BK function has complicated the interpretation of phenotypes involving the interaction of multiple cell types which independently express BK channels. Here, we report the generation of a targeted allele for conditional inactivation of <em>Kcnma1</em> using the Cre-loxP system (<em>Kcnma1fl-tdTomato</em>). Cre-mediated recombination generates a null allele, and BK currents were not detectable in neurons and muscle cells from Nestin-Cre; <em>Kcnma1fl/fl</em> and SM22α-Cre; <em>Kcnma1fl/fl </em>mice, respectively. tdTomato expression was detected in Cre-expressing tissues, but not in Cre-negative controls. These data demonstrate the utility of<em> Kcnma1fl-tdTomato</em> for conditional deletion of the BK channel, facilitating the understanding of tissue-specific contributions to physiological function in vivo.</p>
Allele-specific chromatin accessibility for 23 cancer types and weight files for Regulome Wide Association-Studies (RWAS)
<p><strong>stratAS_results.tar.gz</strong></p> <p>This folder contains the results of analyses of allele-specific chromatin accessibility for 23 cancer types + pan-cancer using the stratAS software. The analyses identified allelically imbalanced genomic regions from 406 cancer ATAC-Seq samples. The files are named after each cancer type (or “pancancer” for the pan-cancer analysis) and contain the following columns:</p> <p>CHR - Chromosome<br> POS - Position of test<br> SNP RSID - ID of test SNP<br> P0 - Start of gene/peak<br> P1 - End of gene/peak<br> NAME - Name of gene/peak<br> CENTER - Center position of peak (or TSS for gene)<br> N.HET - Number of heterozygous individuals tested N.READS - Number of reads tested in total<br> ALL.AF - Allelic fraction estimate from beta binomial test across both conditions<br> ALL.BBINOM.P - Beta-binomial test for imbalance across both conditions<br> C0.AF - Allelic fraction estimate from condition 0<br> C0.BBINOM.P - Beta-binomial test for imbalance in condition 0<br> C1.AF - Allelic fraction estimate from condition 1<br> C1.BBINOM.P - Beta-binomial test for imbalance in condition 1<br> DIFF.BBINOM.P - Beta-binomial test for difference between conditions<br> IND.C0 - Number of each condition 0 individual included in this test (comma separated)<br> IND.C0.COUNT.REF - condition 0 REF allele counts of each individual included in this test (comma separated)<br> IND.C0.COUNT.ALT - condition 0 ALT allele counts of each individual included in this test (comma separated)<br> IND.C1 - Number of each condition 1 individual included in this test (comma separated)<br> IND.C1.COUNT.REF - condition 1 REF allele counts of each individual included in this test (comma separated)<br> IND.C1.COUNT.ALT - condition 1 ALT allele counts of each individual included in this test (comma separated)</p> <p>In our analysis, samples that belong to a cancer type that is analyzed for allelic imbalance are assigned to Condition 1 (C1) while samples belonging to the remaining 22 cancer types are assigned to Condition 0 (C0). For the pan-cancer analysis, samples from all 23 cancer types are assigned to C1. P-values denoting the significance of allelic imbalance in a given cancer type (or pan-cancer analysis) are listed in the column C1.BBINOM.P. P-values denoting the significance of differential allelic imbalance between a given cancer type and the remaining 22 cancer types are listed in column DIFF.BBINOM.P (set to NA for pan-cancer analysis since all samples are assigned to C1).</p> <p>More information about stratAS and its output format can be found at https://github.com/gusevlab/stratAS.</p> <p>The conducted analyses are described in detail in the methods section of Grishin D. and Gusev A. Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms (2022).</p> <p><strong>RWAS_weights.tar.gz</strong></p> <p>This folder contains weight files that can be used together with GWAS summary statistics to conduct Regulome Wide Association-Studies (RWAS) using the FUSION software package.</p> <p>Each weight file corresponds to a single accessible element in the FUSION format. Instructions on how to use FUSION for RWAS can be found at http://gusevlab.org/projects/fusion/. RWAS is conducted in the same manner as TWAS using these RWAS weights.</p> <p>The weight files were generated using a pan-cancer peak set. A BED file containing pan-cancer peaks can be found in the peaks_hg19 folder along with other BED files containing cancer-type specific peaks. Cancer-type specific peak files can be used to restrict the RWAS analysis to regulatory elements active in specific cancer types.</p> <p>The conducted analyses are described in detail in the methods section of Grishin D. and Gusev A. Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms (2022).</p>
Scoring of 13 microsatellite loci for Tetrastigma loheri in Cebu (Philippines) based on the fragment length size of their respective alleles
<p>Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.</p>
HLA class I and class II allelic profile of healthy Lebanese population
<p class="MsoNormal"><strong><span>Background</span></strong><span>. This study examined the origin of present-day Lebanese using high-resolution HLA class I and class II allele and haplotype distributions. The study subjects comprised 152 unrelated individuals, and their HLA class I and class II alleles and two-locus and five-locus haplotypes were compared with those of neighboring and distant communities </span><span>using genetic distances, neighbor-joining dendrograms, correspondence, and<strong> </strong>haplotype analyses</span><span>. </span><span>HLA class I (<em>A</em>, <em>B</em>, <em>C</em>) and class II (<em>DRB1</em>, <em>DQB1</em>) were genotyped at a high-resolution level by PCR-SSP. </span></p> <p class="MsoNormal"><strong><span>Results</span></strong><span>. In total, 76 alleles across the five HLA loci were detected: <em>A*03:01</em> (17.1%), <em>A*24:02</em> (16.5%), <em>B*</em></span><em><span>35:01</span></em><span> (25.7%), <em>C*</em></span><em><span>04:01</span></em><span> (25.3%), and </span><em><span>C*</span></em><em><span>07:01</span></em><span> (20.7%) were t</span><span>he most frequent class I alleles, while <em>DRB1*</em></span><em><span>11:01</span></em><span> (34.2%) and <em>DQB1*03:01</em> (43.8%) were the most frequent class II alleles. All pairs of HLA loci were in significant linkage disequilibrium. The most frequent two-locus haplotypes recorded were <em>DRB1*11:01</em></span><span>~</span><em><span>DQB1*03:01</span></em><span> (30.9%), <em>B*35:01</em>-<em>C*04:01</em> (20.7%), <em>B*35:01</em></span><span>~</span><em><span>DRB1*11:01</span></em><span> (13.8%), and <em>A*24:02</em></span><span>~</span><em><span>B*35:01</span></em><span> (10.3%). Lebanese appear to be closely related to East Mediterranean communities such as Levantines (Palestinians, Syrians, and Jordanians), Turks, Macedonians, and Albanians. However, Lebanese appear to be distinct from North African, Iberian, and Sub-Saharan communities. </span></p> <p class="MsoNormal"><strong><span>Conclusions</span></strong><span>. Collectively, this indicates a limited genetic contribution of Arabic-speaking populations </span><span>(from North Africa or the Arabian Peninsula</span><span>) and Sub-Saharan communities to the present-day Lebanese gene pool.</span><strong><span> </span></strong><span>This confirms the notion that Lebanese population are of mixed East Mediterranean and Asian origin, with a marked European component.</span></p>
Major and minor allele genomes for hg38 using dbSNP151 with precomputed Bowtie and BWA indexes
<p>Minor and major allele genomes for the hg38 reference genome (GRCh38.p12) built using common SNPs from dbSNP release 151. Processing details are described in https://doi.org/10.1101/2022.04.21.488824.</p> <p>The following files are included:</p> <ul> <li>Fasta files for both the major and minor allele genomes</li> <li>Bowtie indexes for both the major and minor allele genomes</li> <li>BWA indexes for both the major and minor allele genomes</li> </ul> <p>The genomes are also available as Bioconductor BSgenome packages:</p> <ul> <li>https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major.html</li> <li>https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor.html</li> </ul> <p> </p>
Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants
<p>In the era of blood group genomics, reference collections of complete and fully-resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (i.e. separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully-resolved sequences for all six main <em>ABO</em> allele groups: <em>ABO</em>*<em>A1</em>/<em>A2</em>/<em>B</em>/<em>O.01.01</em>/<em>O.01.02</em>/<em>O.02</em>. We selected 77 samples from an <em>ABO</em> genotype dataset (n=25,200) of serologically-typed Swiss blood donors. The entire <em>ABO</em> gene was amplified in two overlapping long-range PCRs (covering ~23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, two samples per <em>ABO</em> group were re-sequenced using Illumina and PacBio technology. All 154 full-length <em>ABO</em> sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each <em>ABO</em> group. Most genetic diversity was found between, not within, <em>ABO</em> groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each <em>ABO</em> group. Strikingly, our data uncovered four genetic variants putatively specific for <em>ABO</em>*<em>A1</em>, for which direct diagnostic targets are currently lacking. We validated <em>A1</em>-diagnostic potential using whole-genome data (n=4,872) of a multi-ethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality <em>ABO</em> haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of <em>ABO</em>, as well as studies about the function and evolutionary history of <em>ABO</em>.</p>
Allele scores and frequencies of 66 microsatellite locus loci in Solenopsis geminata
<p>Allele scores and frequencies of 66 microsatellite loci in <em>Solenopsis geminata</em> samples were analyzed from 18 populations and 131 individuals.</p> <p>Eighteen populations were collected from South Korea, Laos, Myanmar, Thailand, and the United States.</p>
Data from: Loci controlling nitrate reductase activity in maize: ultraviolet-B signaling in aerial tissues increases nitrate reductase activity in leaf and root when responsive alleles are present
Environmental factors, such as ultraviolet-B (UV-B) irradiation, have the ability to affect pathways such as nitrogen metabolism. As fixed nitrogen is the keystone mineral nutrient that controls grain crop yield, any alteration in this cycle can be detrimental to plant productivity. Nitrate reductase enzyme activity is responsible for the reduction of nitrate to nitrite, and nitrate is the major form of nitrogen assimilated in plants. In maize (Zea mays L.) production, nitrate assimilation kinetics are important for both high- and low-input agricultural systems. Nitrate reductase protein activity is controlled by phosphatases and kinases. Nitrate reductase activity is responsive to environmental signals such as light–dark cycles and UV-B radiation, although the regulatory controls are not yet fully understood. We have determined the location of maize genetic factors that control nitrate reductase activity and the extent of contribution of each of these factors, both locally in the leaf tissue and via long-distance signaling loci that affect root nitrate reductase activity upon leaf UV irradiation. In the IBM94 recombinant inbred mapping population, the loci controlling regulation of nitrate reductase activity under UV-B map to different positions than the loci controlling nitrate reductase activity in unexposed plants.
Data from: Number of alleles as a predictor of the relative assignment accuracy of STR and SNP baselines for chum salmon
Short tandem repeat (STR) markers, which exhibit many alleles per locus, are commonly used to assign fish to their populations of origin. Single nucleotide polymorphisms (SNPs), which have many technical advantages over STRs, typically exhibit only two alleles per locus. Simulation studies have indicated that number of independent alleles is a good predictor of accuracy of genetic markers for fishery applications. Extant STR baselines for salmon contain hundreds of alleles, and it has been extrapolated that hundreds of SNP markers need to be developed before SNP baselines will compare to these STR baselines. We compared 15 STRs exhibiting 349 independent alleles to 61 SNP assays exhibiting 66 independent alleles for accuracy in assigning to closely related populations of chum salmon. The SNP baseline yielded slightly higher mean accuracies for proportional assignment and comparable accuracies for individual assignment. Overall the SNP baseline performed considerably better, relative to the microsatellite baseline, than predicted based on the number of independent alleles in each baseline. We suggest that this discrepancy is due to the fact that the simulation studies do not capture the impacts of the different strategies commonly employed for discovering and selecting STR and SNP markers.
Data from: Stabilising selection on microsatellite allele length at arginine vasopressin 1a receptor and oxytocin receptor loci
The loci arginine vasopressin receptor 1a (avpr1a) and oxytocin receptor (oxtr) have evolutionarily conserved roles in vertebrate social and sexual behavior. Allelic variation at a microsatellite locus in the 5' regulatory region of these genes is associated with fitness in the bank vole Myodes glareolus. Given the low frequency of long and short alleles at these microsatellite loci in wild bank voles, we used breeding trials to determine whether selection acts against long and short alleles. Female bank voles with intermediate length avpr1a alleles had the highest probability of breeding, while male voles whose avpr1a alleles were very different in length had reduced probability of breeding. Moreover, there was a significant interaction between male and female oxtr genotypes, where potential breeding pairs with dissimilar length alleles had reduced probability of breeding. These data show how genetic variation at microsatellite loci associated with avpr1a and oxtr is associated with fitness, and highlight complex patterns of selection at these loci. More widely, these data show how stabilising selection might act on allele length frequency distributions at gene-associated microsatellite loci.
Data from: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken
The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome-wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity-related genes or both. Here, we tested whether genome-wide heterozygosity (20 990 SNPs) and diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater's prairie-chicken (Tympanuchus cupido attwateri). We found that postrelease survival of captive-bred birds was related to alleles of the innate (Toll-like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome-wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome-wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations and that in some populations specific functional genes may be better predictors of fitness than genome-wide heterozygosity.
gnomAD Allele Frequency SQLite database V2.1.1
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 56G for WGS v3.1.1 (about 760.000.000 variants), and allows scientists to look for minor allele frequencies of variants really fast (A query containing 300.000 variants takes ~40s.) Look here for more information: https://github.com/KalinNonchev/gnomAD_MAF</p> <p>Genomic variant database</p> <p>gnomAD Allele Frequency SQLite database V2.1.1 for hg19</p>
gnomAD Allele Frequency SQLite database V3.1.1
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 56G for WGS v3.1.1 (about 760.000.000 variants), and allows scientists to look for minor allele frequencies of variants really fast (A query containing 300.000 variants takes ~40s.) Look here for more information: https://github.com/KalinNonchev/gnomAD_MAF</p> <p>Genomic - variant database</p> <p>gnomAD Allele Frequency SQLite database V3.1.1 for hg38</p>
Data from: Genetic drift and selection in many-allele range expansions
We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E. coli with differing expansion velocities in radially expanding colonies. We compare experimental measurements of the average fraction, correlation functions between strains, and the relative rates of genetic domain wall annihilations and coalescences to simulations modeling the population as a one-dimensional ring of annihilating and coalescing random walkers with deterministic biases due to selection. The simulations reveal that the evolutionary dynamics can be collapsed onto master curves governed by three essential parameters: (1) an expansion length beyond which selection dominates over genetic drift; (2) a characteristic angular correlation describing the size of genetic domains; and (3) a dimensionless constant quantifying the interplay between a colony's curvature at the frontier and its selection length scale. We measure these parameters with a new technique that precisely measures small selective differences between spatially competing strains and show that our simulations accurately predict the dynamics without additional fitting. Our results suggest that the random walk model can act as a useful predictive tool for describing the evolutionary dynamics of range expansions composed of an arbitrary number of genotypes with different fitnesses.
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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.