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25,372 results for “Transcriptomics”
Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment in order to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (1) investigate transcriptomic divergence as measured by liver RNA-Seq; (2) test the correlation between divergence in expression and sequence polymorphism and (3) investigate the extent of allelic imbalance. We also compared the results of RNA-seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish over-expressed more contigs associated with protein synthesis while dwarf fish over-expressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA-Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele-specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next-generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification
Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species specific amplicon length. Furthermore most of the markers were successfully amplified in other Calanus species allowing the molecular identification of C. helgolandicus, C hyperboreus and C. marshallae.
Data from: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.
Data from: Echidna venom gland transcriptome provides insights into the evolution of monotreme venom
Monotremes (echidna and platypus) are egg-laying mammals. One of their most unique characteristic is that males have venom/crural glands that are seasonally active. Male platypuses produce venom during the breeding season, delivered via spurs, to aid in competition against other males. Echidnas are not able to erect their spurs, but a milky secretion is produced by the gland during the breeding season. The function and molecular composition of echidna venom is as yet unknown. Hence, we compared the deeply sequenced transcriptome of an in-season echidna crural gland to that of a platypus and searched for putative venom genes to provide clues into the function of echidna venom and the evolutionary history of monotreme venom. We found that the echidna venom gland transcriptome was markedly different from the platypus with no correlation between the top 50 most highly expressed genes. Four peptides found in the venom of the platypus were detected in the echidna transcriptome. However, these genes were not highly expressed in echidna, suggesting that they are the remnants of the evolutionary history of the ancestral venom gland. Gene ontology terms associated with the top 100 most highly expressed genes in echidna, showed functional terms associated with steroidal and fatty acid production, suggesting that echidna "venom" may play a role in scent communication during the breeding season. The loss of the ability to erect the spur and other unknown evolutionary forces acting in the echidna lineage resulted in the gradual decay of venom components and the evolution of a new role for the crural gland.
Data from: Transcriptome-derived tetranucleotide microsatellites and their associated genes from the giant panda (Ailuropoda melanoleuca)
Recently, an increasing number of microsatellites or Simple Sequence Repeats (SSRs) have been found and characterized from transcriptome. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In the present work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, four CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these four CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes contained these four CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers would pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda.
Data from: Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53 929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.
Data from: De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.
Adaptation to different ecological environments can promote speciation. Although numerous examples of such 'ecological speciation' exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing reads that assembled into 84,937 contigs representing approximately 18,282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these genomic resources to assess multi-locus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate a first step towards future genomic work in Timema.
Data from: Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation
BACKGROUND: Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato. RESULTS: We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern "switch gene" optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns. CONCLUSIONS: This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.
Data from: De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues
Background: The American lobster, Homarus americanus, is an important species as an economically valuable fishery, a key member in marine ecosystems, and a well-studied model for central pattern generation, the neural networks that control rhythmic motor patterns. Despite multi-faceted scientific interest in this species, currently our genetic resources for the lobster are limited. In this study, we de novo assemble a transcriptome for Homarus americanus using central nervous system (CNS), muscle, and hybrid neurosecretory tissues and compare gene expression across these tissue types. In particular, we focus our analysis on genes relevant to central pattern generation and the identity of the neurons in a neural network, which is defined by combinations of genes distinguishing the neuronal behavior and phenotype, including ion channels, neurotransmitters, neuromodulators, receptors, transcription factors, and other gene products. Results: Using samples from the central nervous system (brain, abdominal ganglia), abdominal muscle, and heart (cardiac ganglia, pericardial organs, muscle), we used RNA-Seq to characterize gene expression patterns across tissues types. We also compared control tissues with those challenged with the neuropeptide proctolin in vivo. Our transcriptome generated 34,813 transcripts with known protein annotations. Of these, 5,000-10,000 of annotated transcripts were significantly differentially expressed (DE) across tissue types. We found 421 transcripts for ion channels and identified receptors and/or proteins for over 20 different neurotransmitters and neuromodulators. Results indicated tissue-specific expression of select neuromodulator (allostatin, myomodulin, octopamine, nitric oxide) and neurotransmitter (glutamate, acetylcholine) pathways. We also identify differential expression of ion channel families, including kainite family glutamate receptors, inward-rectifying K+ (IRK) channels, and transient receptor potential (TRP) A family channels, across central pattern generating tissues. Conclusions: Our transcriptome-wide profiles of the rhythmic pattern generating abdominal and cardiac nervous systems in Homarus americanus reveal candidates for neuronal features that drive the production of motor output in these systems.
Invasion history shapes host transcriptomic response to a body-snatching parasite
<p>By shuffling biogeographic distributions, biological invasions can both disrupt long-standing associations between hosts and parasites and establish new ones. This creates natural experiments with which to study the ecology and evolution of host-parasite interactions. In estuaries of the Gulf of Mexico, the white-fingered mud crab (Rhithropanopeus harrisii) is infected by a native parasitic barnacle Loxothylacus panopaei (Rhizocephala), which manipulates host physiology and behavior. In the 1960s, L. panopaei was introduced to the Chesapeake Bay and has since expanded along the southeastern Atlantic coast, while host populations in the northeast have so far been spared. We use this system to test the host's transcriptomic response to parasitic infection and investigate how this response varies with the parasite's invasion history, comparing populations representing (1) long-term sympatry between host and parasite, (2) new associations where the parasite has invaded during the last sixty years, and (3) naïve hosts without prior exposure. A comparison of parasitized and control crabs revealed a core response, with widespread downregulation of transcripts involved in immunity and molting. The transcriptional response differed between hosts from the parasite's native range and where it is absent, consistent with previous observations of increased susceptibility in populations lacking exposure to the parasite. Crabs from the parasite's introduced range, where prevalence is highest, displayed the most dissimilar response, possibly reflecting immune priming. These results provide molecular evidence for parasitic manipulation of host phenotype and the role of gene regulation in mediating host-parasite interactions.</p>
Data from: Neighborhood defense gene similarity effects on tree performance: a community transcriptomic approach
The structure and dynamics of ecological communities are ultimately the outcome of the differential demographic rates of individuals. Individual growth and mortality rates largely result from the interaction between an organism's phenotype and the abiotic and biotic environment. Functional traits have been used extensively over the past decade to elucidate links among phenotypes, demography and community dynamics. A fundamental weakness of most functional trait approaches is the use of 'soft' traits associated with resource acquisition to examine how neighbourhood similarity affects tree survival and growth. However, these 'soft' traits are unlikely to be good predictors of similarities among co-occurring species. Less easily measured aspects of organismal function – such as those related to defence – have frequently gone unmeasured. This is particularly problematic for testing important hypotheses in forest ecology, such as the Janzen–Connell hypothesis where focal trees are expected to be at a disadvantage if their neighbours share the same natural enemies. A potential alternative to functional trait approaches is to quantify the transcriptomic or functional genomic similarity of species. Such analyses are now possible in natural systems where de novo transciptome assemblies can be used to conduct functional phylogenomic analyses where homologous gene trees are produced. Using demographic plot data for 21 species from a North American forest dynamic plot, we conduct a community functional phylogenomic analysis of a plant community to elucidate the similarity in defence response genes across species. This similarity was then used to ask whether the similarity in defence genes of heterospecific species in the local neighbourhood of a focal individual tree influences its growth and mortality rates. The results show that individual growth rates are higher when surrounded by dissimilar heterospecific species for 16 of 27 defence genes analysed. Additionally, survival rates are increased when an individual is in a neighbourhood with dissimilar species for 4 of the 27 defence genes studied. Lastly, strong conspecific effects were found in all analyses, underscoring that future analyses investigating the genetic variation and differential expression of defence-related genes in neighbourhoods may prove important. Synthesis. In summary, this research leverages recent advances in RNA sequencing and bioinformatics to conduct community-wide transcriptomic analyses and analyses of defence-related gene similarity across a tree community. The results demonstrate that defence gene similarity in neighbourhoods often does have negative effects on individual demographic performance as predicted by the Janzen–Connell hypothesis.
Data from: Transcriptomic responses to conspecific and congeneric competition in co-occurring Trifolium
Species coexistence requires differential response to inter- and intraspecific competition, typically conceptualized as niche differentiation. Coexistence of close relatives therefore poses an interesting scenario with regards to niche differentiation since these species generally have many traits in common due to shared ancestry. Native Californian Trifolium assemblages are locally diverse and represent a unique system for understanding competitive interactions among close relatives. We conducted two similar greenhouse studies in which Trifolium fucatum was grown alone, with a conspecific competitor, and with a congeneric competitor (Trifolium macraei). In the first study, we assessed biomass production in T. fucatum, and in the second study we conducted an RNAseq analysis of T. fucatum roots to test for differentially expressed genes that may mediate competitive interactions and potentially coexistence. Compared to plants grown alone, competition (i.e. growth in the same pot) with a conspecific resulted in a greater reduction in biomass than competition with a congener, as predicted by theory. However, competition with a congener resulted in twice as many differentially expressed genes as competition with a conspecific. Annotations of identified genes differentiating congeneric from conspecific competition suggest several functions attributed to interactions with third-party organisms, including nodulation with rhizobial mutualists, and defence responses against pathogens and herbivores. In addition, salt-responsive genes and an iron transporter were differentially expressed in congeneric competition, and comparisons of sodium and iron concentrations in field soils where these species are found showed that T. fucatum occurs in higher sodium and iron microsites than T. macraei. Thus, the transcriptome highlighted abiotic niche axes worth pursuing in future ecological experiments as potential mediators of coexistence. We also found a subset of genes that responded similarly to both congeneric and conspecific competition in both direction and magnitude, indicating some conserved responses to competition, regardless of neighbour identity. Synthesis. Transcriptomic analyses represent novel tools for identifying the molecular mechanisms underlying interactions among species. Working iteratively with ecological experimentation and observation, transcriptomes may allow us to identify novel dimensions of the n-dimensional niche that determine species' distributions and their ability to coexist.
Data from: Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement
Background: Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement. Results In maize and teosinte, 13,593 highly conserved genes, including 12,030 multiexonic genes, were detected. By identifying AS isoforms from mutliexonic genes, we found that AS types were not significantly different between maize and teosinte. In addition, the two main AS types (intron retention and alternative acceptor) contributed to more than 60% of the AS events in the two species, but the average unique AS events per each alternatively spliced gene in maize (4.12) was higher than that in teosinte (2.26). Moreover, 94 genes generating 98 retained introns with transposable element (TE) sequences were detected in maize, which is far more than 9 retained introns with TEs detected in teosinte. This indicates that TE insertion might be an important mechanism for intron retention in maize. Additionally, the AS levels of 3864 genes were significantly different between maize and teosinte. Of these, 151 AS level-altered genes that are involved in transcriptional regulation and in stress responses are located in regions that have been targets of selection during maize improvement. These genes were inferred to be putatively improved genes. Conclusions We suggest that both maize and teosinte share similar AS mechanisms, but more genes have increased AS complexity during domestication from teosinte to maize. Importantly, a subset of AS level-increased genes that encode transcription factors and stress-responsive proteins may have been selected during maize improvement.
Data from: Global transcriptome changes in perennial ryegrass during early infection by pink snow mould
Lack of resistance to pink snow mould (Microdochium nivale) is a major constraint for adaptation of perennial ryegrass (Lolium perenne L.) to continental regions with long-lasting snow cover at higher latitudes. Almost all investigations of genetic variation in resistance have been performed using cold acclimated plants. However, there may be variation in resistance mechanisms that are functioning independently of cold acclimation. In this study our aim was to identify candidate genes involved in such resistance mechanisms. We first characterized variation in resistance to M. nivale among non-acclimated genotypes from the Norwegian cultivar 'Fagerlin' based on relative regrowth and fungal quantification by real-time qPCR. One resistant and one susceptible genotype were selected for transcriptome analysis using paired-end sequencing by Illumina Hiseq 2000. Transcriptome profiles, GO enrichment and KEGG pathway analysis indicate that defense response related genes are differentially expressed between the resistant and the susceptible genotype. A significant up-regulation of defense related genes, as well as genes involved in cell wall cellulose metabolic processes and aryl-alcohol dehydrogenase (NADP+) activity, was observed in the resistant genotype. The candidate genes identified in this study might be potential molecular marker resources for breeding perennial ryegrass cultivars with improved resistance to pink snow mould.
Transcript expression data. Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes
<p>To advance understanding of the mechanistic factors regulating cassava flowering, the leaf transcriptomes at 1) two stages of plant development were compared in two genotypes at Ubiaja and Ibadan, Nigeria; and 2) three controlled-environment growth chambers.</p>
[MIRROR] transcriptome assemblies for SOAPdenovo-Trans paper
<p>mirrored from ftp://public.genomics.org.cn/BGI/SOAPdenovo-Trans/SOAPdenovo-Trans_Supplementary_Assemblies.tar.gz to provide a faster CDN</p>
Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing - Image and In SItu Sequencing data
<p>Image and ISS data for Spatial transcriptome mapping of the desmoplastic growth pattern of colorectal liver metastases by in situ sequencing reveals a biologically relevant zonation of the desmoplastic rim.</p><p>Image data consists of:</p><ul><li>Nucler stain (DAPI)</li><li>Masks for liver, rim and tumor regions</li><li>H&E images of parallel tissue sections</li></ul><p>Gene and cluster marker data is collected in the <i>markers.h5ad</i> file which can be read using AnnData (<a href="https://anndata.readthedocs.io/en/latest/">https://anndata.readthedocs.io/en/latest/)</a>. </p><p> </p>
Global Transcriptomic Analysis of Placenta from Women with Gestational SARS-CoV-2 Infection during the 3rd Trimester of Pregnancy
<p>Supplementary data for <strong>Global Transcriptomic Analysis of Placenta from Women with Gestational SARS-CoV-2 Infection during the 3rd Trimester </strong><br><strong>of Pregnancy</strong></p>
spatiAlign: An Unsupervised Contrastive Learning Model for Data Integration of Spatially Resolved Transcriptomics
<p>Integrative analysis of spatially resolved transcriptomics datasets empowers a deeper understanding of complex biological systems. However, integrating multiple tissue sections presents challenges for batch effect removal, particularly when the sections are measured by various technologies or collected at different times. Here, we propose spatiAlign, an unsupervised contrastive learning model that employs the expression of all measured genes and the spatial location of cells, to integrate multiple tissue sections. It enables the joint downstream analysis of multiple datasets not only in low-dimensional embeddings but also in the reconstructed full expression space. In benchmarking analysis, spatiAlign outperforms state-of-the-art methods in learning joint and discriminative representations for tissue sections, each potentially characterized by complex batch effects or distinct biological characteristics. Furthermore, we demonstrate the benefits of spatiAlign for the integrative analysis of time-series brain sections, including spatial clustering, differential expression analysis, and particularly trajectory inference that requires a corrected gene expression matrix.</p>
Polystyrene-induced changes in adipose transcriptome
<p>Microplastics (MP) derived from the weathering of polymers, or synthesized in this size range, have become widespread environmental contaminants and have found their way into water supplies and the food chain. Despite this awareness, little is known about the health consequences of MP ingestion. We have previously shown that the consumption of polystyrene (PS) beads was associated with intestinal dysbiosis, diabetes, and obesity in mice. To further evaluate the systemic metabolic effects of PS on the gut-liver-adipose tissue axis, we supplied C57BL/6J mice with normal water or that containing two sizes of PS beads (0.5mm and 5mm) at a concentration of 1mg/ml. After 13wk, we evaluated several indices of metabolism and liver function. As previously observed, mice drinking the PS-containing water had a potentiated weight gain and adipose expansion. Here we found that this was associated with an increased abundance of adipose F4/80<sup>+</sup> macrophages. These exposures did not cause non-alcoholic fatty liver disease (NAFLD) but were associated with decreased liver:body weight ratios and an enrichment in hepatic FXR and LXR signaling. PS also increased hepatic cholesterol and altered both hepatic and cecal bile acids. Mice consuming PS beads and treated with the berry anthrocyanin, delphinidin, demonstrated an attenuated weight gain compared to those mice receiving a control intervention and also exhibited a down-regulation of cAMP and PPAR signaling pathways. This study highlights the obesogenic role of PS in perturbing the gut-liver-adipose axis and altering nuclear receptor signaling and intermediary metabolism. Dietary interventions may limit the adverse metabolic effects of PS consumption. </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.