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12,455 results for “Promoters”
Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans
<p>Dedicated genetic pathways regulate cysteine homeostasis. For example, high levels of cysteine activate cysteine dioxygenase, a key enzyme in cysteine catabolism in most animal and many fungal species. The mechanism by which cysteine dioxygenase is regulated is largely unknown. In an unbiased genetic screen for mutations that activate cysteine dioxygenase (<em>cdo-1</em>) in the nematode <em>C. elegans, </em>we isolated loss-of-function mutations in <em>rhy-1 </em>and <em>egl-9, </em>which encode proteins that negatively regulate the stability or activity of the oxygen-sensing hypoxia-inducible transcription factor (<em>hif-1</em>). EGL-9 and HIF-1 are core members of the conserved eukaryotic hypoxia response. However, we demonstrate that the mechanism of HIF-1-mediated induction of <em>cdo-1 </em>is largely independent of EGL-9 prolyl hydroxylase activity and the von Hippel-Lindau E3 ubiquitin ligase, the classical hypoxia signaling pathway components. We demonstrate that <em>C. elegans cdo-1 </em>is transcriptionally activated by high levels of cysteine and <em>hif-1</em>. <em>hif-1-</em>dependent activation of <em>cdo-1</em> occurs downstream of an H<sub>2</sub>S-sensing pathway that includes <em>rhy-1, cysl-1, </em>and <em>egl-9.</em> <em>cdo-1 </em>transcription is primarily activated in the hypodermis where it is also sufficient to drive sulfur amino acid metabolism. Thus, the regulation of <em>cdo-1 </em>by <em>hif-1 </em>reveals a negative feedback loop that maintains cysteine homeostasis. High levels of cysteine stimulate the production of an H<sub>2</sub>S signal. H<sub>2</sub>S then acts through the <em>rhy-1/cysl-1/egl-9 </em>signaling pathway to increase HIF-1-mediated transcription of <em>cdo-1, </em>promoting the degradation of cysteine via CDO-1.</p>
Data for: Does parasitoid species diversity promote protective symbiont diversity?
<p>How does diversity in nature come about? One factor contributing to this diversity are species interactions; diversity on one trophic level can shape diversity on lower or higher trophic levels. For example, parasite diversity enhances host immune diversity. Protective symbionts mediate host resistance and are therefore also engaged in reciprocal selection with their host's parasites. Here, we applied experimental evolution in a well-known symbiont-aphid-parasitoid system to study whether parasitoid diversity contributes to maintaining symbiont diversity. We used caged populations of black bean aphids (<em>Aphis fabae</em>), containing uninfected individuals and individuals infected with different strains of the bacterial endosymbiont <em>Hamiltonella defensa, </em>which protects aphids against parasitoids. Over multiple generations, these populations were exposed to three different species of parasitoid wasps (<em>Aphidius colemani</em>, <em>Binodoxys acalephae</em>, or <em>Lysiphlebus fabarum</em>), simultaneous or sequential mixtures of these species, or no wasps. Surprisingly, we observed little selection for <em>H. defensa</em> in most treatments, even when it clearly provided protection against a fatal parasitoid infection. This seemed to be caused by high induced costs of resistance: aphids surviving parasitoid attacks suffered an extreme reduction in fitness. In marked contrast to previous studies looking at the effect of different genotypes of a single parasitoid species, we found little evidence for a diversifying effect of multiple parasitoid species on symbiont diversity in hosts.</p>
Applying innovative cloud computing technology for the effective management of Groundwater resources to promote SUStainable food security within the Sokoto Basin, Nigeria (AGSUS)
Open the record for dataset details and reuse information.
Data from: The maintenance and emergence of diversity promotes open-ended evolution in a prebiotic context
<p>This data was collected during the study entitled “The maintenance and emergence of diversity promotes open-ended evolution in a prebiotic context."<br> <br>We explored how selective contexts shape the evolution of innovation, using <em>in vitro </em>selection with single-stranded DNA (ssDNA) as an empirical model for pre-cellular evolution. During this selection regime, a diverse pool of 76-bp ssDNA (consisting of a random 40-nt region, flanked by 18-nt primer binding sites) was incubated with a target substrate, during which sequences were able to bind to the substrate. Following incubation, unbound sequences were discarded, while bound sequences were partitioned and amplified via PCR and used in subsequent rounds of selection. <br> <br>Our experimental design consisted of 8 cycles of selection with either streptavidin-coated magnetic beads or yeast cells (<em>Kluyveromyces lactis</em>) as the binding substrate. We also included two variable selection regimes, where four rounds of selection were completed with one substrate before switching to the other target for the remaining four rounds (3 replicate populations per treatment). All replicates from rounds 1, 4, 7, and 8 were purified and submitted for next-generation sequencing (Illumina NovaSeq S4 2x150-bp lane), along with the random starting library. Sequencing generated a mean of 29,741,261 pair-end reads per sample, which were assembled and normalized to ~100,000 reads per sample used for analysis, which are included here.<br> <br>The file names are organized in the following format: Selection Treatment_Round of Selection_Replicate #. For example, “Beads_R1_1” indicates a population that was selected with beads as the binding substrate following Round 1 of selection, replicate population 1 (out of 3 replicates). Scripts used to list contigs (<em>EditFastas.l</em>) and measure the frequencies of each sequence (<em>CountSeqs.l</em> ) are also included.</p>
Roadside disturbance promotes plant communities with arbuscular mycorrhizal associations in mountain regions worldwide
<p><em>Aim: </em>We aimed to assess the impact of road disturbances on the dominant mycorrhizal types in ecosystems at the global level and how this mechanism can potentially lead to lasting plant community changes.</p> <p><em>Location: </em>Globally distributed mountain regions</p> <p><em>Time Period:</em> 2007-2018 Taxa studied: Plants (linked to their associated mycorrhizal fungi)</p> <p><em>Methods:</em> We used a database of coordinated plant community surveys following mountain roads from 894 plots in 11 mountain regions across the globe in combination with an existing database of mycorrhizal-plant associations in order to approximate the relative abundance of mycorrhizal types in natural and disturbed environments.</p> <p><em>Results:</em> Our findings show that roadside disturbance promotes the cover of plants associated with arbuscular mycorrhizal (AM) fungi. This effect is especially strong in colder mountain environments and in mountain regions where plant communities are dominated by ectomycorrhizal (EcM) or ericoid-mycorrhizal (ErM) associations. Furthermore, non-native plant species, which we confirmed to be mostly AM plants, are more successful in environments dominated by AM associations.</p> <p><em>Main Conclusions:</em> These biogeographical patterns suggest that changes in mycorrhizal types could be a crucial factor in the worldwide impact of anthropogenic disturbances on mountain ecosystems. Indeed, roadsides foster AM-dominated systems, where AM-fungi might aid AM-associated plant species while potentially reducing the biotic resistance against invasive non-native species, often also associated with AM networks. Restoration efforts in mountain ecosystems will have to contend with changes in the fundamental make-up of EcM- and ErM plant communities induced by roadside disturbance.</p>
Data from: Land-use intensity and relatedness to native plants promote exotic plant invasion in a tropical biodiversity hotspot
<p>Exotic plant invasions threaten biodiversity and are costly to farmers. Land use is a major pathway promoting the spread of exotic plant species; however, little is known about the processes underlying the success of exotic plants in tropical agricultural landscapes. Focussing on the heterogeneous smallholder landscapes of north-eastern Madagascar, we studied exotic plants of understorey communities across a land-use intensity gradient from unburned lands (old-growth forests, forest fragments, and forest-derived vanilla agroforests) to burned ones (fallow-derived vanilla agroforests, woody fallows, and herbaceous fallows). </p> <p>We quantified the absolute species richness, abundance, and cover of exotic plants across land-use types and their proportional contribution to community richness, abundance, and cover as indicators of exotic plant invasion. We tested for the effects of land-use parameters, namely land-use history, canopy closure, and landscape-level forest cover, on exotic plants. Additionally, we tested whether the phylogenetic relatedness between exotic and native species in the same plot affected invasion success, testing Darwin's naturalization and pre-adaptation hypotheses. </p> <p>All indicators of exotic plant invasion were lowest in old-growth forests and forest fragments and highest in fallow-derived vanilla agroforests, woody fallows, and herbaceous fallows. Absolute and proportional exotic richness was negatively affected by canopy closure, and landscapes with high forest cover had lower proportions of exotic plant richness. High phylogenetic relatedness between exotics and natives was associated with lower proportional richness but higher proportions of exotics in abundance and cover. However, individual exotic species showed contrasting responses to land-use parameters and relatedness to natives.</p> <p>Synthesis and applications: Our results indicate that maintaining unburned lands, land-use types with dense canopies, and landscapes with high forest cover prevents the spread of exotic plants within agricultural landscapes of north-eastern Madagascar. Supporting Darwin's pre-adaptation hypothesis, exotic plants phylogenetically closely related to native plants are more likely to become successful invaders in terms of abundance and cover. Nevertheless, individual species show different responses to land-use changes and phylogenetic relatedness. Therefore, land-use decisions and management choices can be tailored to limit the spread of exotic species and to preserve native plants in this global biodiversity hotspot.</p>
Promoter methylation leads to Hepatocyte Nuclear Factor 4A loss and pancreatic cancer aggressiveness.
<p><i>Efforts to decode pancreatic ductal adenocarcinoma (PDAC) heterogeneity and the consequent therapeutic selection remains a challenge. We aimed to characterize epigenetically regulated pathways involved in PDAC progression.</i></p><p><i>Global DNA methylation analysis in pancreatic cancer patient tissues and cell lines was performed to identify differentially methylated genes. Targeted bisulfite sequencing and in vitro methylation reporter assays were employed to investigate the direct link between sitespecific methylation and transcriptional regulation. A series of in vitro loss- and gain-of function studies, and in vivo xenograft and the KPC (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre) mouse models were used to assess pancreatic cancer cell properties. Gene and protein expression analyses were performed in three different cohorts of pancreatic cancer patients and correlated to clinicopathological parameters.</i></p><p><i>We identify Hepatocyte Nuclear Factor 4A (HNF4A) as a novel target of hypermethylation in pancreatic cancer and demonstrate that site-specific proximal promoter methylation drives HNF4A transcriptional repression. Expression analyses in patients, indicate the methylation-associated suppression of HNF4A expression in pancreatic cancer tissues. In vitro and in vivo studies reveal that HNF4A is a novel tumor suppressor in pancreatic cancer, regulating cancer growth and aggressiveness. As evidenced in both the KPC mouse model and human pancreatic cancer tissues, HNF4A expression declines significantly in the early stages of the disease. Most importantly, HNF4 loss correlates with poor overall patient survival.</i></p>
AF2 models for "Co-translational assembly promotes functional diversification of paralogous proteins" by Mallik, et al.
<p>AF2 models used for analyses presented in "Co-translational assembly promotes functional diversification of paralogous proteins" by Saurav Mallik, Angel F. Cisneros, Christian R. Landry, and Emmanuel D. Levy.</p> <p>These models were used to analyze the structural divergence of 3703 Obligatory Homomer, 697 Mixed, and 181 Obligatory Heteromer pairs.</p> <p>Folders are separated into different categories:<br>- Models of homomers (from Schweke et al., 2024. Cell):<br> . AF2_HM_full_models: Full structures of homodimeric models.<br> . AF2_HM_nodiso3: Core structures of homomeric models, trimmed using scripts from Schweke et al. (2023).</p> <p>- Models of heteromers (generated in this work):<br> . AF2_HET_full_models: Full structures of heterodimeric models.<br> . AF2_HET_nodiso3: Core structures of heteromeric models, trimmed using a modified version of the code from Schweke et al. (2023) to work with heterodimers.</p>
The co-inhibitory receptor TIGIT promotes tissue protective functions in T cells
<p>TIGIT KO and wild-type mouse T cells were sorted and collected from the lung and spleen in steady state and LCMV conditions. Briefly, cells were sorted into three sub-populations and subsequently pooled for scRNAseq. The individual subpopulations were CD3+/CD8+, CD3+/CD4+/Foxp3-, and CD3+/CD4+/Foxp3+.</p> <p>tigit-full-dataset.rds: contains the full processed dataset ~198645 cells and 25906 genes formatted as a Seurat (v5) object. </p> <p>Alternatively, the raw data plus the associated metadata can be loaded with the following 3 files:</p> <p>tigit-raw-counts.mtx.gz: A sparse count matrix used in the Seurat object above. The matrix was stored as a matrix market format and was subsequently gzipped. The matrix is expected to have 198645 cells and 25906 features.</p> <p>cell-metadata.csv: Cell metadata found in the seu@meta.data slot of the Seurat object.</p> <p>gene-metadata.csv: gene metadata of the scRNAseq experiment as found in the seu@assays$RNA@meta.features slot of the Seurat object.</p> <p> </p>
Mitochondrial oxidant stress promotes alpha-synuclein aggregation and spreading in mice with mutated glucocerebrosidase
<p>These are the data sets and plasmid sequences of the viral vectors used in the study "Mitochondrial oxidant stress promotes alpha-synuclein aggregation and spreading in mice with mutated glucocerebrosidase"</p>
How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study - Second part
<p>Second part of the data deposition for the paper "<strong>How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study</strong>", by Lemmens et al. Part one is availible via <a href="https://doi.org/10.5281/zenodo.13929049">10.5281/zenodo.13929049</a></p>
Woodland, cropland and hedgerows promote pollinator abundance in intensive grassland landscapes, with saturating benefits of flower cover
<p>To enable reproduction of analyses in the linked journal article, we provide a table of habitats, woody linear features and elevation of all pollinator survey transect sections. This table can be linked to the publicly available data, based on square ID and section ID, to reproduce the analyses (except for one discontinued square with ID marked 'NA' in the publicly available data).</p> <p>Journal article abstract:</p> <p>1. Pollinating insects provide economic value by improving crop yield. They are also functionally and culturally important across ecosystems outside of cropland. To understand landscape-level drivers of pollinator declines, and guide policy and intervention to reverse declines, studies must cover (1) multiple insect and plant taxa and (2) a range of agricultural and semi-natural land uses. Furthermore, in an era of woodland restoration initiatives and rewilding ideologies, the contribution of woodland and woody linear features (WLFs; e.g. hedgerows) to pollinator abundance demands further investigation. 2. We demonstrate fine-scale analysis of high-quality, co-located measurements from a national environmental survey. We relate pollinator transect counts to ground-truth habitat and WLF maps across 300 1km squares in Wales, UK. We look at effects of habitat type, flower cover, WLF density and habitat diversity on summer abundance (July and August) of eight insect groups, representing three insect orders (Lepidoptera, Hymenoptera and Diptera). 3. Compared with improved grassland (the dominant habitat in Wales), pollinator abundance is consistently higher in cropland and woodland - especially broadleaved woodland. For solitary bees and two hoverfly groups, abundance is predicted to be at least 1.5× higher in woodland ecosystems than elsewhere. Furthermore, we estimate contributions of WLFs to abundance in agriculturally improved habitats to be up to 14% for honeybees and up to 21% for hoverflies. 4. The abundance of all insect groups increases with flower cover, which is a key mechanism through which woodland, cropland and grassland support pollinators. Importantly, we observe diminishing returns of increasing flower cover for abundance of non-Apis pollinator groups, expecting roughly twice the increase in abundance per % flower cover from 0-5%, as compared with 10-15%. However, the shape of the relationship was inverted for honeybees, which showed steeper increases in abundance at higher flower cover. 5. Synthesis & applications: We provide a holistic view of the drivers of pollinator abundance in Wales, in which flower cover, woodland, WLFs and cropland are critical. We propose a key role for woodland creation, hedge-laying and farmland heterogeneity within future land management incentive schemes. Finally, we suggest targeting of interventions to maximise benefits for non-Apis pollinators. Specifically, increasing floral provision in areas where existing flower cover is low – e.g. in flower-poor improved grasslands - could effectively increase pollinator abundance and diversity, while prioritising wild over managed species.</p>
Identifying behavioral and attitudinal barriers and drivers to promote consumption of pulses: A quantitative survey across five European countries
<p>Even though pulses are nutritious and environmentally friendly high-protein crops, they are commonly regarded as old-fashioned. Consumption of pulses is low in developed countries, and it has received very limited attention in agricultural and behavioral research over the past years. Based on a pan-European survey, the present study aims to provide extensive insights into consumer perceptions towards pulses. The objective is to identify effective measures to increase consumer acceptance of pulses, and thus potentially increase their share in the daily diets across Europe. Quantitative data was collected in May 2020 through a web-based survey conducted in five different European countries, Germany, Denmark, Spain, Poland, and the United Kingdom (N = 4,916). Quota-based sampling was used to ensure comparability across samples and wide coverage in terms of age, gender, and locality of residence. Using cluster analysis with a subsequent logistic regression, cross-cultural differences were found in terms of relatively high consumption of pulses among Spanish respondents, somewhat lower for Polish, German and UK respondents, and even lower among Danish respondents. Drivers of consumption significantly differed across surveyed samples, mainly being health first, followed by sensory preferences. For respondents from Poland, Spain, and Germany the main reason for not consuming pulses related to problems with digestion, whereas in the Danish and UK samples a neglect related to preparation. Future product development as well as increased information about nutrition and cooking of pulses could potentially increase consumer acceptance. Though, considering cross-cultural differences is important when developing strategies to promote consumption of pulses.</p>
Polyploidy promotes divergent evolution across the leaf economics spectrum and plant edaphic niche in the Dianthus broteri complex
<ol> <li>The evolution of the leaf economics spectrum (LES) is known to be constrained by genetic relatedness but also promoted at small geographic and phylogenetic scales. In those cases, we hypothesised that polyploidy would play a prominent role as an outstanding source of functional divergence and adaptive potential.</li> <li>We registered leaf-level nutrient, water and light economy related traits from the LES as well as edaphic properties in the four cytotypes of the autopolyploid <i>Dianthus broteri</i> complex (2×, 4×, 6× and 12×). We analysed the effect of ploidy level on the integration of the LES network, checked if concerted evolution occurred between LES and soil niche and tested the influence of phylogeny on the variables. Alternative evolutionary models for both sets of traits were compared.</li> <li> <span>We found higher divergence of polyploids (especially 6</span>×<span> and 12</span>×<span>) compared to diploids</span> in the LES and soil niche, but these traits are not coevolving. <span>6</span>×<span> and 12</span>× showed opposite ecological strategies regarding resource use and higher uncoupling of the LES network. Early divergence of traits prevailed in both LES and edaphic niche (supported by better fitted evolutionary models with one optimum per cytotype), but post-polyploidization processes played an important role for the photochemical behaviour.</li> <li> <i>Synthesis.</i><b> </b><span>Our results indicated shifts in ecological strategies across <i>D. broteri</i> cytotypes and suggested a powerful role of polyploidy in overcoming constraints for the evolution of plant functional traits.</span> </li> </ol>
Non-centrosomal microtubules at kinetochores promote rapid chromosome biorientation during mitosis in human cells
<p>Kinetochore tracking data associated with "Non-centrosomal microtubules at kinetochores promote rapid chromosome biorientation during mitosis in human cells" by Renda, Miles, et al., Current Biology, 2022.</p> <p>Contact Alexey Khodjakov at alexey.khodjakov@health.ny.gov for any questions or processing routines.</p> <p>Each file contains coordinates of centrioles and kinetochores in a single cell. </p> <p>Key to variables:</p> <p>ao -- time point corresponding to anaphase onset</p> <p>cell_id -- comprises three parts: cell type_treatment_number (NaN when only first 15 min of prometaphase were tracked).</p> <p>centrioles -- coordinates of centrioles. Two pages correspond to the two centrosomes, first three columns are X-Y-Z of the mother and the second three columns are X-Y-Z of the daughter centrioles</p> <p>kinetochores -- coordinates of kinetochores. Each page corresponds to a chromosome. X-Y-Z coordinates of sister kinetochores are in columns 1-3 and 4-6.</p> <p>neb -- time point corresponding to nuclear envelope breakdown.</p> <p>total_chrs -- number of chromosomes in the cell</p> <p>tracked -- number of tracks obtained in the cell</p>
Supplementary materials of Brain Extract of Subacute Traumatic Brain Injury Promotes Neuronal Differentiation of Human Neural Stem Cells Via Autophagy
<p>Figure S1: Characterization of hNSCs. In proliferate medium, the embryo derived hNSCs could form the neurospheres (A). Markers of NSCs (NES, SOX2, SOX1) were detected (B). The SOX2<sup>+</sup> cells accounted for >95% of all cells (C). Bar scale: 60μm;</p> <p>Figure S2: The proliferation of hNSCs in TBI brain extracts with different phases. Differentiated hNSCs could be labeled with EdU in TBI brain extracts with different phases (A). Ratio of EdU<sup>+</sup> cells was decreased with the progression of days post-injury (B). Bar scale: 75μm; ****: P<0.0001;</p> <p>Figure S3: The GO annotations and KEGG pathway analysis of different expressed pro-teins in acute brain extract and subacute brain extract;</p> <p>Table S1: The protein profiles of brain extract in acute phase and subacute phase after TBI.</p>
Raw Data for the article: Extracellular Vesicle-Derived microRNAs of Human Wharton's Jelly Mesenchymal Stromal Cells May Activate Endogenous VEGF-A to Promote Angiogenesis
<p>Despite low levels of vascular endothelial growth factor (VEGF)-A, the secretome of human Wharton's jelly (WJ) mesenchymal stromal cells (MSCs) effectively promoted proangiogenic responses in vitro, which were impaired upon the depletion of small (~140 nm) extracellular vesicles (EVs). The isolated EVs shared the low VEGF-A profile of the secretome and expressed five microRNAs, which were upregulated compared to fetal dermal MSC-derived EVs. These upregulated microRNAs exclusively targeted the <em>VEGF-A</em> gene within 54 Gene Ontology (GO) biological processes, 18 of which are associated with angiogenesis. Moreover, 15 microRNAs of WJ-MSC-derived EVs were highly expressed (Ct value ≤ 26) and exclusively targeted the thrombospondin 1 (<em>THBS1</em>) gene within 75 GO biological processes, 30 of which are associated with the regulation of tissue repair. The relationship between predicted microRNA target genes and WJ-MSC-derived EVs was shown by treating human umbilical-vein endothelial cells (HUVECs) with appropriate doses of EVs. The exposure of HUVECs to EVs for 72 h significantly enhanced the release of VEGF-A and THBS1 protein expression compared to untreated control cells. Finally, WJ-MSC-derived EVs stimulated in vitro tube formation along with the migration and proliferation of HUVECs. Our findings can contribute to a better understanding of the molecular mechanisms underlying the proangiogenic responses induced by human umbilical cord-derived MSCs, suggesting a key regulatory role for microRNAs delivered by EVs.</p>
Raw experiment data from: Homogeneity of agriculture landscape promotes insecticide resistance in the ground beetle Poecilus cupreus
<p>This dataset is raw research data related to the paper published in PLOS ONE: Sowa et al. 2022, Homogeneity of agriculture landscape promotes insecticide resistance in the ground beetle <em>Poecilus cupreus</em>; <a href="https://doi.org/10.1371/journal.pone.0266453">https://doi.org/10.1371/journal.pone.0266453</a></p>
GIS4Schools promotional video
<p>The GIS4Schools promotional video introduces briefly the structure of the project, main objectives and outputs. </p> <p>It is available also in Italia, Spanish, Portuguese, Catalan and Romanian in the official youtube channel of the project: </p> <p>https://www.youtube.com/channel/UCBStKUqwPRA9VbRR9VMWPNw/featured </p>
CAGE and txrevise promoter usage QTL summary statistics
<p>This dataset contains promoter usage QTL summary statistics obtained using <a href="https://github.com/eQTL-Catalogue/qtlmap">QTLmap</a>. QTLmap_summary_CAGE.txt contains summary statistics for CAGE, QTLmap_summary_txrevise-25.txt for regular <a href="https://github.com/kauralasoo/txrevise">txrevise</a> and QTLmap_summary_txrevise-supplemented-20.txt for txrevise with the new generated annotations.</p> <p>This dataset contains the promoter annotations obtained with CAGE as part of the FANTOM5 project, cleaned and reformatted using <a href="https://github.com/andreasvija/cage/blob/master/qtlmap_prep/clean_promoters.R">this code</a> for the purpose of QTL mapping, that were used to obtain the aforementioned summary statistics. They can be found in Cleaned_FANTOM5_promoter_annotations.tsv.</p> <p> </p> <p>QTL summary statistics column descriptions:</p> <p>molecular_trait_object_id - gene</p> <p>molecular_trait_id - top promoter for the gene</p> <p>n_traits - how many promoters were tested for the gene</p> <p>n_variants - how many genetic variants were tested for the promoter</p> <p>variant - top genetic variant for the promoter</p> <p>chromosome - chromosome</p> <p>position - promoter's top genetic variant start position</p> <p>pvalue - nominal p-value of the association between the promoter and genetic variant</p> <p>beta - the fitted linear model's regression coefficent</p> <p>p_perm - empirical p-value calculated using permutations</p> <p>p_beta - estimated empirical p-value based on the beta distribution, this is the recommended p-value column</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.