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1,715 results for “Arabidopsis thaliana; Arabidopsis”
Arabidopsis BioCON evolutionary study:Arabidopsis thaliana, Bromus inermis phenotypic selection analyses standardized across trtmnts
We know a lot about the potential ecological effects of increasing concentrations to atmospheric CO2; however, we know relatively little about whether increased concentrations will also affect evolution. In collaboration with Jennifer Lau (KBS and Michigan State University), Peter Reich (U of MN Forestry) and Ruth Shaw (U of MN EEB) we are using a combination traditional quantitative genetic and QTL approaches to determine the effect elevated CO2 has on; patterns of selection, responses to selection, and the genetic basis of phenotypic variation.
Ground truth annotations for top-view images of Arabidopsis thaliana
<ul> <li>ara_rosetteSet.tar.gz contains ground truth annotations for ordinary leaves (used to train model A of the <a href="https://doi.org/10.5281/zenodo.3946320">aradeepopsis pipeline</a>)</li> <li>ara_senescentSet.tar.gz contains ground truth annotations for ordinary and senescent leaves (used to train model B of the <a href="https://doi.org/10.5281/zenodo.3946320">aradeepopsis pipeline</a>)</li> <li>ara_anthoSet.tar.gz contains ground truth annotations for ordinary, senescent and anthocyanin-rich leaves (used to train model C of the <a href="https://doi.org/10.5281/zenodo.3946320">aradeepopsis pipeline</a>)</li> </ul>
Dataset - A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress
<p>Plant immunity is often negatively impacted by heat stress. However, the underlying molecular mechanisms remain poorly characterized. Based on a genome-wide association mapping approach, this study aims to identify in <em>Arabidopsis thaliana</em> the genetic bases of robust resistance mechanisms to the devastating pathogen<em> Ralstonia solanacearum</em> under heat stress. A local mapping population was phenotyped against the <em>R. solanacearum</em> GMI1000 strain at 27 and 30 °C. To obtain a precise description of the genetic architecture underlying natural variation of quantitative disease resistance (QDR), we applied a genome-wide local score analysis. Alongside an extensive genetic variation found in this local population at both temperatures, we observed a playful dynamics of quantitative trait loci along the infection stages. In addition, a complex genetic network of interacting loci could be detected at 30 °C. As a first step to investigate the underlying molecular mechanisms, the atypical meiotic cyclin <em>SOLO DANCERS</em> gene was validated by a reverse genetic approach as involved in QDR to <em>R. solanacearum </em>at 30 °C. In the context of climate change, the complex genetic architecture underlying QDR under heat stress in a local mapping population revealed candidate genes with diverse molecular functions.</p>
Data from: A nested association mapping panel in Arabidopsis thaliana for mapping and characterizing genetic architecture
<p><span><span><span><span><span><span><span><span><span><span><span>Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred populations (RILs) of <i>Arabidopsis thaliana</i>, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.</span></span></span></span></span></span></span></span></span></span></span></p>
Phenotype pictures of Arabidopsis thaliana in high light and low light conditions
<p>The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. The observed variation was validated in a field experiment conducted under natural conditions. All genotypes grew markedly wider rosettes when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were strongly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between Europe and the distantly related populations of China is smaller than the variation observed within Europe indicating that plant growth is constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.</p>
Data from: Activation of the Arabidopsis thaliana immune system by combinations of common ACD6 alleles
A fundamental question in biology is how multicellular organisms distinguish self and non-self. The ability to make this distinction allows animals and plants to detect and respond to pathogens without triggering immune reactions directed against their own cells. In plants, inappropriate self-recognition results in the autonomous activation of the immune system, causing affected individuals to grow less well. These plants also suffer from spontaneous cell death, but are at the same time more resistant to pathogens. Known causes for such autonomous activation of the immune system are hyperactive alleles of immune regulators, or epistatic interactions between immune regulators and unlinked genes. We have discovered a third class, in which the Arabidopsis thaliana immune system is activated by interactions between natural alleles at a single locus, ACCELERATED CELL DEATH 6 (ACD6). There are two main types of these interacting alleles, one of which has evolved recently by partial resurrection of a pseudogene, and each type includes multiple functional variants. Most previously studies hybrid necrosis cases involve rare alleles found in geographically unrelated populations. These two types of ACD6 alleles instead occur at low frequency throughout the range of the species, and have risen to high frequency in the Northeast of Spain, suggesting a role in local adaptation. In addition, such hybrids occur in these populations in the wild. The extensive functional variation among ACD6 alleles points to a central role of this locus in fine-tuning pathogen defenses in natural populations.
Data from: Water availability as an agent of selection in introduced populations of Arabidopsis thaliana: impacts on flowering time evolution
Flowering is one of the most influential events in the life history of a plant and one of the main determinants of reproductive investment and lifetime fitness. It is also a highly complex trait controlled by dozens of genes. Understanding the selective pressures influencing time to flowering, and being able to reliably predict how it will evolve in novel environments, are unsolved challenges for plant evolutionary geneticists. Using the model plant species, Arabidopsis thaliana, we examined the impact of simulated high and low winter precipitation levels on the flowering time of naturalized lines from across the eastern portion of the introduced North American range, and the fitness consequences of early versus late flowering. Flowering time order was significantly correlated across two environments—in a previous common garden experiment and in environmental chambers set to mimic mid-range photoperiod and temperature conditions. Plants in low water flowered earlier, had fewer basal branches and produced fewer fruits. Selection in both treatments favored earlier flowering and more basal branches. Our analyses revealed an interaction between flowering time and water treatment for fitness, where flowering later was more deleterious for fitness in the low water treatment. Our results are consistent with the hypothesis that differences in winter precipitation levels are one of the selective agents underlying a flowering time cline in introduced A. thaliana populations.
Data from: Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions
The study of the evolutionary and population genetics of quantitative traits requires the assessment of within- and among-population patterns of variation. We carried out experiments including eight Iberian Arabidopsis thaliana populations (10 individuals per population) in glasshouse and field conditions. We quantified among- and within-population variation for flowering time and for several field life-history traits. Individuals were genotyped with microsatellites, single nucleotide polymorphisms and four well-known flowering genes (FRI, FLC, CRY2 and PHYC). Phenotypic and genotypic data were used to conduct QST–FST comparisons. Life-history traits varied significantly among- and within-populations. Flowering time also showed substantial within- and among-population variation as well as significant genotype × environment interactions among the various conditions. Individuals bearing FRI truncations exhibited reduced recruitment in field conditions and differential flowering time behavior across experimental conditions, suggesting that FRI contributes to the observed significant genotype × environment interactions. Flowering time estimated in field conditions was the only trait showing significantly higher quantitative genetic differentiation than neutral genetic differentiation values. Overall, our results show that these A. thaliana populations are genetically more differentiated for flowering time than for neutral markers, suggesting that flowering time is likely to be under divergent selection.
Data from: Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana
As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations - i.e., is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of MA lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype-environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype-environment interaction would increase the amount of genetic variation maintained by mutation-selection balance.
Data from: Heterosis and outbreeding depression in crosses between natural populations of Arabidopsis thaliana
Understanding the causes and architecture of genetic differentiation between natural populations is of central importance in evolutionary biology. Crosses between natural populations can result in heterosis if recessive or nearly recessive deleterious mutations have become fixed within populations because of genetic drift. Divergence between populations can also result in outbreeding depression because of genetic incompatibilities. The net fitness consequences of between-population crosses will be a balance between heterosis and outbreeding depression. We estimated the magnitude of heterosis and outbreeding depression in the highly selfing model plant Arabidopsis thaliana, by crossing replicate line pairs from two sets of natural populations (C↔R, B↔S) separated by similar geographic distances (Italy↔Sweden). We examined the contribution of different modes of gene action to overall differences in estimates of lifetime fitness and fitness components using joint scaling tests with parental, reciprocal F1 and F2, and backcross lines. One of these population pairs (C↔R) was previously demonstrated to be locally adapted, but locally maladaptive quantitative trait loci were also found, suggesting a role for genetic drift in shaping adaptive variation. We found markedly different genetic architectures for fitness and fitness components in the two sets of populations. In one (C↔R), there were consistently positive effects of dominance, indicating the masking of recessive or nearly recessive deleterious mutations that had become fixed by genetic drift. The other set (B↔S) exhibited outbreeding depression because of negative dominance effects. Additional studies are needed to explore the molecular genetic basis of heterosis and outbreeding depression, and how their magnitudes vary across environments.
Data from: Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate
Arabidopsis thaliana inhabits diverse climates and exhibits varied phenology across its range. Although A. thaliana is an extremely-well studied model species, the relationship between geography, growing season climate and its genetic variation is poorly characterized. We used redundancy analysis (RDA) to quantify the association of genomic variation [214,051 single nucleotide polymorphisms (SNPs)] with geography and climate among 1,003 accessions collected from 447 locations in Eurasia. We identified climate variables most correlated with genomic variation, which may be important selective gradients related to local adaptation across the species range. Climate variation among sites of origin explained slightly more genomic variation than geographical distance. Large-scale spatial gradients and early spring temperatures explained the most genomic variation, while growing season and summer conditions explained the most after controlling for spatial structure. SNP variation in Scandinavia showed the greatest climate structure among regions, possibly because of relatively consistent phenology and life history of populations in this region. Climate variation explained more variation among non-synonymous SNPs than expected by chance, suggesting that much of the climatic structure of SNP correlations is due to changes in coding sequence that may underlie local adaptation.
Data from: Conflicting selection on the timing of germination in a natural population of Arabidopsis thaliana
The timing of germination is a key life-history trait that may strongly influence plant fitness and that sets the stage for selection on traits expressed later in the life cycle. In seasonal environments, the period favourable for germination and the total length of the growing season are limited. The optimal timing of germination may therefore be governed by conflicting selection through survival and fecundity. We conducted a field experiment to examine the effects of timing of germination on survival, fecundity and overall fitness in a natural population of the annual herb Arabidopsis thaliana in north-central Sweden. Seedlings were transplanted at three different times in late summer and in autumn covering the period of seed germination in the study population. Early germination was associated with low seedling survival, but also with high survival and fecundity among established plants. The advantages of germinating early more than balanced the disadvantage and selection favoured early germination. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination and that the optimal timing of germination should vary in space and time as a function of the direction and strength of selection acting during different life-history stages.
Data from: Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis thaliana
Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via comparison of gene coexpression networks, implemented as an R package called machine learning–based differential network analysis (mlDNA) and apply this method to reanalyze a set of abiotic stress expression data in Arabidopsis thaliana. The mlDNA first used a ML-based filtering process to remove nonexpressed, constitutively expressed, or non-stress-responsive "noninformative" genes prior to network construction, through learning the patterns of 32 expression characteristics of known stress-related genes. The retained "informative" genes were subsequently analyzed by ML-based network comparison to predict candidate stress-related genes showing expression and network differences between control and stress networks, based on 33 network topological characteristics. Comparative evaluation of the network-centric and gene-centric analytic methods showed that mlDNA substantially outperformed traditional statistical testing–based differential expression analysis at identifying stress-related genes, with markedly improved prediction accuracy. To experimentally validate the mlDNA predictions, we selected 89 candidates out of the 1784 predicted salt stress–related genes with available SALK T-DNA mutagenesis lines for phenotypic screening and identified two previously unreported genes, mutants of which showed salt-sensitive phenotypes.
Data from: An ecological history of the relict genetic lineage of Arabidopsis thaliana
The combination of extensive population sampling with whole-genome sequencing in the annual plant Arabidopsis thaliana has recently allowed the identification of a genetically differentiated relict lineage. The most important nuclei of relict A. thaliana is found in the Iberian Peninsula and North Africa, although relict accessions have also been found scattered across Atlantic oceanic islands, eastern Mediterranean Basin, South and East Africa and China. We hypothesised that relict A. thaliana long survived and adapted to a wide array of environments in the Iberian Peninsula and North Africa due to the fact that the region repeatedly acted as glacial refugia. Given the lack of evidence to support this hypothesis, we addressed this issue by studying the ecological history of Iberian and North African relict A. thaliana. To this end, we analysed the relationship between the current habitat suitability of relict A. thaliana, estimated with species distribution models, and the vegetation dynamics in the region over the last millennia using pollen fossil data from sediment cores and reconstructions of past distribution ranges of the most important tree species occurring in the region. Overall, our results indicated that a higher current habitat suitability of relict A. thaliana was correlated with more stable vegetation dynamics since the Last Glacial Maximum and during the Holocene. Given that relict A. thaliana is known to harbour genetic variation specific to its relict nature, we also evaluated the differentiation between relict and non-relict A. thaliana accessions at the functional genetic level for the known flowering genes, CRY2 and TSF. Genomic surveys detected the existence of haplogroups of these genes occurring at very high frequency only among relict accessions. Overall, our study reinforced the relict character of this lineage thought to be at the base of the species' early history. We stress the need to sample in depth other geographic areas harbouring relict A. thaliana and conduct further functional genetic analyses between relict and non-relict accessions to keep disentangling the evolutionary trajectory of this annual plant.
Data from: Spatio-temporal variation in fitness responses to contrasting environments in Arabidopsis thaliana
The evolutionary response of organisms to global climate change is expected to be strongly conditioned by pre-existing standing genetic variation. In addition, natural selection imposed by global climate change on fitness-related traits can be heterogeneous over time. We estimated selection of life-history traits of an entire genetic lineage of the plant A. thaliana occurring in north-western Iberian Peninsula that were transplanted over multiple years into two environmentally contrasting field sites in southern Spain, as southern environments are expected to move progressively northwards with climate change in the Iberian Peninsula. The results indicated that natural selection on flowering time prevailed over that on recruitment. Selection favored early flowering in six of eight experiments and late flowering in the other two. Such heterogeneity of selection for flowering time might be a powerful mechanism for maintaining genetic diversity in the long run. We also found that north-western A. thaliana accessions from warmer environments exhibited higher fitness and higher phenotypic plasticity for flowering time in southern experimental facilities. Overall, our transplant experiments suggested that north-western Iberian A. thaliana has the means to cope with increasingly warmer environments in the region as predicted by trends in global climate change models.
Data from: Transgenerational effects of mild heat in Arabidopsis thaliana show strong genotype specificity that is explained by climate at origin
Transgenerational environmental effects can trigger strong phenotypic variation. However, it is unclear how cues from different preceding generations interact. Also, little is known about genetic variation for these life-history-traits. Here we present effects of grandparental and parental mild heat, and their combination, on four traits of the third-generation phenotype of 14 Arabidopsis thaliana genotypes. We tested for correlations of these effects with climate and constructed a conceptual model to identify the environmental conditions that favour the parental effect on flowering time. We observed strong evidence for genotype-specific transgenerational effects. On average, A. thaliana accustomed to mild heat, producing more seeds after two generations. Parental effects overruled grandparental effects in all traits but reproductive biomass. Flowering was generally accelerated by all transgenerational effects. Notably, the parental effect triggered earliest flowering in genotypes adapted to dry summers. Accordingly, this parental effect was favoured in the model when early summer heat terminated the growing season and environments were correlated across generations. Our results suggest that A. thaliana can partly accustom to mild heat over two generations and genotype-specific parental effects show non-random evolutionary divergence across populations that may support climate change adaptation in the Mediterranean.
Data from: Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome
The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints, but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the 'environmental relevance' of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study.
Transcriptional and epigenetic profiling of Arabidopsis thaliana exposed to low dose ionizing radiation
<p>RNA and methylation profiling of Arabidopsis seedlings to low dose ionizing radiation</p>
cDNA sequence of E2 gene family in Arabidopsis thaliana and data of statistical analysis
<p>E2 ubiquitin-conjugating enzymes act as a heart role in the ubiquitination process and are responsible for catalysis ubiquitin transfer. Although the function of ubiquitin-protein ligases (E3s) in plant response to diverse abiotic stress by targeting specific substrates has been well studied, the E2s' involvement in environmental responses and their downstream targets are not well understood. Here, we demonstrated that the E2 ubiquitin-conjugating enzyme 18 (UBC18) regulates the stability of FREE1 to modulate iron deficiency stress. UBC18 affects the ubiquitination of FREE1 and promotes its degradation, overexpression of<em> UBC18</em> in plants decreases their sensitivity to iron deficiency by reducing the level of FREE1, and high accumulation of FREE1 in<em> </em>the<em> ubc18</em> mutant resulted in sensitivity to iron deficiency. In addition, we demonstrated the lysine residues K227, K295, K315, and K540 are required for FREE1 ubiquitination and stability regulation, and mutation of these lysines of FREE1 residues resulted in sensitivity to iron starvation in plants. Taken together, our findings reveal a mechanism of UBC18 in response to iron deficiency stress by altering the abundance of FREE1, and further elucidate the role of ubiquitination sites in FREE1 stability regulation and the plant iron deficiency response.</p>
Transposable element products, functions, and regulatory networks in Arabidopsis thaliana
<h1>README</h1> <p>This dataset includes the main outputs from the work titled <strong>Transposable element products, functions, and regulatory networks in <em>Arabidopsis thaliana</em>.</strong></p> <h2><strong>Summary</strong></h2> <p>Transposable elements (TEs) are DNA sequences with the ability to propagate themselves within and across genomes. Their mobilization is catalyzed by self-encoded factors, yet these factors have been poorly investigated due to difficulties in defining TE genes in genomes. Here, we leveraged extensive long- and short-read transcriptome data, together with structural predictions, transcription factor binding site identification, and transcriptional network analyses, to construct a comprehensive atlas of TE transcripts and TE-encoded products in the model organism <em>Arabidopsis thaliana</em>. We uncovered hundreds of transcriptionally competent TEs, each potentially encoding multiple proteins either through distinct genes, alternative splicing, or post-translational processing. Structural-based protein analyses revealed dozens of hitherto unidentified domains of unknown function, enabling us to predict proteins with multimerization and DNA binding domains forming macromolecular complexes involved in transposition. Furthermore, we demonstrate that TE expression is highly intertwined with the transcriptional network of cellular genes, and identified transcription factors and cis-regulatory elements associated with their coordinated expression during development or in response to environmental cues. This comprehensive atlas of TE-genes and TE-proteins provides a valuable resource for studying the mechanisms involved in transposition and their consequences for genome and organismal function.</p> <h2><strong>File description</strong></h2> <p>It includes the following data:</p> <ol> <li><code>annots/TE_Functional_Annotation.Borreda2024.gtf</code> - Annotation file including Arabidopsis TEs and TE-genes. TE-genes defined in our work are indicated in the 'Source' column of the gtf. TAIR10-defined TEs for whom we did not annotate new transcripts are also included.</li> <li><code>seqs</code> - This folders includes all the transcript sequences (cDNAs.tsv) and the first and longest ORFs found in each of them (prot.csv), which were used for further analyses. The specific copy, gene, isoform and, in the case of proteins, ORF, is indicated for each sequence.</li> <li><code>structures</code> - The zipped folder <code>full_length_prots_pdbs.zip</code> includes all the 3D structures from full-length TE proteins. Note that identical proteins, which would result in identical structures, have been collapsed to reduce the total dataset size; equivalences can be found in <code>identical_proteins</code>.</li> <li><code>structures/SD_Cluster_Functions.tsv</code> - We clustered all Structural Domains (SD) based on 3D similarity and assigned a function to each cluster based on the database hits. This table indicated, for each of these SDs, to which cluster it belongs, the superfamily, family and element containing it, the number of Conserved Domains included within it and the number of hits with resolved (retrieved from the RCSB-PDB database) or predicted (AlphaFold2) protein structures. The last column includes the putative function assigned to each cluster.</li> <li><code>coexpression</code> - Coexpressed genes were classiffied into modules using WGCNA. In the table <code>Gene_Modules.tsv</code> we include, for each gene and TE-gene (provided it has expression in at least one sample, see methods on the publication for details), the TE family and superfamily when applicable and the module to which it belongs. The modules were named based on the results of the GO enrichment analysis of the genes contained. The results of this GO enrichment are included in <code>GO_Enrichment.tsv</code>, where we include the main funciton of the associated GOs, the number of entries and TE-genes within the module, a list of GO terms enriched in that specific module and finally a list of TE families enriched in each module.</li> <li><code>dapseq</code> - We reanalized the DAP-seq dataset from O'Malley 2016, selecting only TFBS with a binding site within a DAP-seq peak. The list of filtered peaks we found is reported in <code>DAPseq_TFBS_Motifs.tsv</code>. The columns include the coordinates of the TFBS (which have been filtered to fall within a DAP-seq peak and include the TFBS motif), the strand of the motif, the score of the motif reported by FIMO, the motif sequence, the Sequence Read identified for the original DAP-seq data, and the family, name and gene of the TF associated with that specific peak.</li> </ol>
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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.