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15,277 results for “GENETIC”
RDF Linked Data representation of GC-MS data from the 'Rose Genome' article published in Nature genetics, June, 2018
<p>This dataset corresponds to the RDF Linked Data representation of the measurements of 61 known metabolites (all annotated with resolvable CHEBI identifiers and InChi strings), measured by gas chromatography mass-spectrometry (GC-MS) in 6 different Rose cultivars (all annotated with resolvable NCBITaxonomy Identifiers) and 3 organism parts (all annotated with resolvable Plant Ontology identifiers). The quantitation types are annotated with resolvable <a href="https://github.com/ISA-tools/stato">STATO</a> terms. Most of the semantics resources belong to the <a href="http://obofoundry.org">OBO foundry</a>.</p> <p>The transformation to RDF was performed on a Frictionless Tabular Data Package (<a href="https://frictionlessdata.io/specs/tabular-data-package/">https://frictionlessdata.io/specs/tabular-data-package/)</a>, holding the data extracted from a supplementary material table, available from <a href="https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-018-0110-3/MediaObjects/41588_2018_110_MOESM3_ESM.zip">https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-018-0110-3/MediaObjects/41588_2018_110_MOESM3_ESM.zip</a> and published alongside the Nature Genetics manuscript identified by the following doi: <a href="https://doi.org/10.1038/s41588-018-0110-3">https://doi.org/10.1038/s41588-018-0110-3</a>, published in June 2018. This supplementary material table was deposited to Zenodo and is identified by the following doi: <a href="https://doi.org/10.5281/zenodo.2598799">https://doi.org/10.5281/zenodo.2598799</a></p> <p>This dataset is used to demonstrate how to make data Findable, Accessible, Discoverable and Interoperable (FAIR) and how Frictionless Tabular Data Package representations can be easily mobilised for reanalysis and data science.</p> <p>It is associated to the following project: <a href="https://github.com/proccaserra/rose2018ng-notebook">https://github.com/proccaserra/rose2018ng-notebook</a> with all the necessary information, executable code and tutorials in the form of Jupyter notebooks.</p>
Example Dataset for npstat: Population genetics from Pooled NGS data NPStat v1: User guide
<p>Example Dataset for npstat to test the program and the different options.</p> <p>The example dataset contains a pileup file with sequences of of the 2L chromosome from fifteen pooled inbreed individuals of <em>Drosophila melanogaster </em>(<span>doi: 10.1038/nature10811</span>). The dataset also contains the sequence reference of the 2L chromosome in fasta format, an outgroup sequence in fasta format of <em>D. yakuba</em> (SRR26246471), a GFF3 annotation file and a file with a brief list of selected SNPs to be analyzed.</p>
Genetic Variants Representation Learning (GV-Rep)
<p>This dataset is used for Genetic Variants (GV) representation learning. </p>
Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors
<p>Summary statistics for chromatin accessibility and gene expression quantitative trait loci (ca/eQTLs) from Matoba, N., Le, B.D., Valone, J.M. <em>et al.</em> Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors. <em>Nat Neurosci</em> (2024). https://doi.org/10.1038/s41593-024-01773-6</p>
Genetic Modulation of Protein Expression in Rat Brain
<p><span>Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits. However, the fundamental genetic architecture and variation of protein expression have received comparatively less attention than either mRNA or classical phenotypes. In this study, we systematically quantified proteins in the brains of a large family of rats using tandem mass tag (TMT)-based quantitative mass-spectrometry (MS) technology. We identified and quantified a comprehensive proteome of 8,119 proteins from Spontaneously Hypertensive (SHR/Olalpcv), Brown Norway with polydactyly-luxate (BN-Lx/Cub), and 29 of their fully inbred HXB/BXH progeny. Differential expression (DE) analysis identified 597 proteins with significant differences in expression between the parental strains (fold change > 2 and FDR < 0.01). We characterized 95 variant peptides by proteogenomics approach and discovered 464 proteins linked to strong <em>cis</em>-acting quantitative trait loci (pQTLs, FDR < 0.05). We also explored the linkage of pQTLs with behavioral phenotypes in rats and examined the sex-specific pQTLs to reveal both distinct and shared <em>cis</em>-pQTLs between sexes. Furthermore, by creating a novel view of the rat pangenome, we improved the ability to pinpoint candidate genes underlying pQTL. Finally, we explored the connection between the pQTLs in rat and human disorders, underscoring the translational potential of our findings. Collectively, this work demonstrates the value of large and systematic proteo-genetic datasets in understanding protein modulation in the brain and its functional linkage to complex central nervous system (CNS) traits.</span><span> </span></p>
Tree mortality risks under climate change in Europe: assessment of silviculture practices and genetic conservation networks
<p>General context: Climate change can positively or negatively affect abiotic and biotic drivers of tree mortality. Process-based models integrating these climatic effects are only seldom used at species distribution scale.</p> <p>Objective: The main objective of this study was to investigate the multi-causal mortality risk of five major European forest tree species across their distribution range from an ecophysiological perspective, to quantify the impact of forest management practices on this risk and to identify threats on the genetic conservation network.</p> <p><br> Methods: We used the process-based ecophysiological model CASTANEA to simulate the mortality risk of \textit{Fagus sylvatica}, \textit{Quercus petraea}, \textit{Pinus sylvestris}, \textit{Pinus pinaster} and \textit{Picea abies} under current and future climate conditions, while considering local silviculture practices. The mortality risk was assessed by a composite risk index \textit{(CRIM)} integrating the risks of carbon starvation, hydraulic failure and frost damage. We took into account extreme climatic events with the \textit{CRIM$_{max}$}, computed as the maximum annual value of the \textit{CRIM}.</p> <p><br> Results: The physiological processes' contributions to \textit{CRIM} differed among species: it was mainly driven by hydraulic failure for \textit{P. sylvestris} and \textit{Q. petraea}, by frost damage for \textit{P. abies}, by carbon starvation for \textit{P. pinaster}, and by a combination of hydraulic failure and frost damage for \textit{F. sylvatica}. Under future climate, projection showed an increase of \textit{CRIM} for \textit{P. pinaster} but a decrease for \textit{P. abies}, \textit{Q. petraea} and \textit{F. sylvatica}, and little variation for \textit{P. sylvestris}. Under the harshest future climatic scenario, forest management decreased the mean \textit{CRIM} for \textit{P. sylvestris}, increased it for \textit{P. abies} and \textit{P. pinaster} and had no major impact for the two broadleaved species. By the year 2100, 38\% to 90\% of the conservation units are at extinction threat (\textit{CRIM$_{max}$}=1), depending on the species.</p> <p><br> Conclusions: Using a process-based ecophysiological model allowed us to disentangle the multiple drivers of tree mortality under current and future climate. Taking into account the positive effect of increased CO$_2$ on fertilization and water use efficiency, the average risks may increase or decrease in the future depending on species and sites. However, considering extreme climatic events, future projections are as pessimistic than those obtained with bioclimatic niche models.</p> <p> </p> <p>Abbreviation for column:</p> <p>X Longitude<br> Y Latitude<br> LAImax Leaf area index max reach<br> Nha Density per hectar<br> Vha Volume per hectar<br> NEE Net ecosystem exchange<br> NPP net primary production<br> Reco Respiration ecosystem<br> GPP Gross primary production<br> Etveg Evapotranspiration canopy<br> Etsol Evapotranspiration sol<br> TR tree transpiration<br> ETP evapotranspiration potentiel<br> BiomassOfReserves Biomass of reserve<br> rw ring width<br> dbh diameter at breast heast<br> height height<br> BBday Budburst date<br> rFD risk of frost<br> CRIM_max Maximum combined risk index of mortality reach<br> rNSC risk of carbon starvation<br> rPLC risk of embolism<br> rPLC_max Maximum risk of embolism reach<br> CRIM combined risk index of mortality<br> Climate Climatic model<br> rNSC_max maximum risk of carbon starvation reach<br> rFD_max Maximum risk of frost reach<br> Scenario_Sylvicol null means no silvulcture simulated<br> species species<br> Country Country<br> alt_watch altitude of climate simulated<br> grid_watch number of the pixel point of WATCH<br> grid_eurocordex number of the pixel point of Eurocordex<br> Pinus_sylvestris 0 abscence ; 1 presence<br> Fagus_sylvatica 0 abscence ; 1 presence<br> Quercus_petraea 0 abscence ; 1 presence<br> Picea_abies 0 abscence ; 1 presence<br> Pinus_pinaster 0 abscence ; 1 presence</p> <p> </p>
Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya
<p>A large number of undiscovered fungal species still exist on earth, which can be useful for bioprospecting, particularly for single cell oil (SCO) production. <em>Mortierella</em> is one of the significant genera in this field and contains about hundred species. Moreover, <em>M. alpina </em>is the main single cell oil producer / arachidonic acid producer at commercial scale under this genus.</p>
Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".
<p><em>The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l.</em></p> <p>File <strong>"Genetic and clinical data"</strong>:</p> <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (<em>CFH, CD46, CFI, C3, CFB </em>and <em>THBD</em>), the presence of <em>CFH-CFHR</em> genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of <em>CFH-H3</em> and <em>CD46<sub>GGAAC</sub></em> risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> <p>In the file <strong>"C3 and C5b-9 deposition"</strong> is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel<sup>2 </sup>per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5.</p> <p>In the file <strong>"CD46 protein expression"</strong> are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control.</p> <p>In the ppt file <strong>"cDNA amplification and sequencing results"</strong> is reported:</p> <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> <p>Additional data will be made available by the authors, without undue reservation, to any qualified researcher. </p>
Genetic and epigenetic regulation of zebrafish intestinal development
<p>This dataset contains zebrafish (<em>Danio rerio</em>) raw RNA and ChIP (paired-end) sequencing data:</p> <ul> <li>RNA-seq <ul> <li>lane1_BSwt5dpf*: 3 biological replicates of RNA-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>lane1_BSwt7dpf*: 3 biological replicates of RNA-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>lane1_BSwt9dpf*: 3 biological replicates of RNA-seq data from 9dpf wild-type (AB background) pooled intestines</li> </ul> </li> <li>ChIP-seq <ul> <li>Cldn-wt-int-5dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-5dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-5dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> </ul> </li> </ul>
Supplemental data from: Nature or nurture: A genetic basis for the behavioral selection of depth in siscowet and lean lake charr (Salvelinus namaycush) ecomorphs
<p>These files contain the raw depth and temperature sensor data from siscowet and lean lake charr (<em>Salvelinus namaycush</em>) ecomorphs tagged with pop-up satellite archival tags (PSATs). These fish were produced from wild gametes taken from Lake Superior and reared in a common garden study for nine years and then tagged with PSATs and released in southern Lake Superior. The dataset is supplemental to:</p> <p>Goetz, F., Sitar, S., Seider, M., and Jasonowicz, A. 2022. Nature or nurture: A genetic basis for the behavioral selection of depth in siscowet and lean lake charr (<em>Salvelinus namaycush</em>) ecomorphs. Canadian Journal of Fisheries and Aquatic Sciences. (in press).</p> <p><strong>Data description for metadata.csv:</strong></p> <p>This file contains the metadata associated with each tag deployment. This includes biological data as well as key mission paramters.</p> <table> <thead> <tr> <td>Column</td> <td>Type</td> <td>Description</td> </tr> </thead> <tbody> <tr> <td>mission_id</td> <td>integer</td> <td>mission identifier</td> </tr> <tr> <td>tag_sn</td> <td>integer</td> <td>tag serial number</td> </tr> <tr> <td>ecotype</td> <td>string</td> <td>lake trout ecotype</td> </tr> <tr> <td>release_date</td> <td>string</td> <td>date of tag release</td> </tr> <tr> <td>length_mm</td> <td>float</td> <td>total length in mm</td> </tr> <tr> <td>weight_g</td> <td>float</td> <td>weight in g</td> </tr> <tr> <td>lipid</td> <td>float</td> <td>lipid level meadured by Distell fatmeter set in research mode</td> </tr> <tr> <td>release_site</td> <td>string</td> <td>release site (deep or shallow site)</td> </tr> <tr> <td>sampling_rate</td> <td>string</td> <td>sampling interval of tag (format=HH:MM:SS)</td> </tr> <tr> <td>mission_end_utc</td> <td>datetime</td> <td>programmed tag pop off date and time in UTC time (format=YYYY-MM-DD HH:MM:SS)</td> </tr> <tr> <td>notes</td> <td>string</td> <td>notes and comments</td> </tr> </tbody> </table> <p> </p> <p><strong>Data description for the raw sensor data files:</strong></p> <p>The raw sensor data is found in the files that are prefixed with "raw-sensor-data". The data for each tag is in contained in a seperate file and the files are named as follows "raw-sensor-data-{<em><strong>mission_identifier</strong></em>}-{<em><strong>tag_serial_number</strong></em>}.csv".</p> <table> <thead> <tr> <td>Column</td> <td>Type</td> <td>Description</td> </tr> </thead> <tbody> <tr> <td>mission_id</td> <td>integer</td> <td>mission identifier</td> </tr> <tr> <td>tag_sn</td> <td>integer</td> <td>tag serial number</td> </tr> <tr> <td>timestamp_utc</td> <td>datetime</td> <td>timestamp of sensor reading (format=YYYY-MM-DD HH:MM:SS)</td> </tr> <tr> <td>depth_m</td> <td>string</td> <td>depth in meters</td> </tr> <tr> <td>temperature_c</td> <td>string</td> <td>temperature in degrees celcius</td> </tr> </tbody> </table>
Human pancreatic islet microRNAs implicated in diabetes and related traits by large-scale genetic analysis
<p>Genetic studies have identified ≥240 loci associated with risk of type 2 diabetes (T2D), yet most of these loci lie in non-coding regions, masking the underlying molecular mechanisms. Recent studies investigating mRNA expression in human pancreatic islets have yielded important insights into the molecular drivers of normal islet function and T2D pathophysiology. However, similar studies investigating microRNA (miRNA) expression remain limited. Here, we present data from 63 individuals, the largest sequencing-based analysis of miRNA expression in human islets to date. We characterize the genetic regulation of miRNA expression by decomposing the expression of highly heritable miRNAs into <em>cis</em>- and <em>trans</em>-acting genetic components and mapping <em>cis</em>-acting loci associated with miRNA expression (miRNA-eQTLs). We find (i) 84 heritable miRNAs, primarily regulated by <em>trans</em>-acting genetic effects, and (ii) 5 miRNA-eQTLs. We also use several different strategies to identify T2D-associated miRNAs. First, we colocalize miRNA-eQTLs with genetic loci associated with T2D and multiple glycemic traits, identifying one miRNA, miR-1908, that shares genetic signals for blood glucose and glycated hemoglobin (HbA1c). Next, we intersect miRNA seed regions and predicted target sites with credible set SNPs associated with T2D and glycemic traits and find 32 miRNAs that may have altered binding and function due to disrupted seed regions. Finally, we perform differential expression analysis and identify 14 miRNAs associated with T2D status—including miR-187-3p, miR-21-5p, miR-668, and miR-199b-5p—and 4 miRNAs associated with a polygenic score for HbA1c levels—miR-216a, miR-25, miR-30a-3p, and miR-30a-5p.</p>
Attack of the clones: population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose
<p><em>Colletotrichum lupini</em>, causing lupin anthracnose, is one of the worst pathogens to lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics and molecular basis of host interaction of this notorious lupin pathogen. A collection of globally representative <em>C. lupini </em>isolates was genotyped through triple digest restriction-site associated DNA sequencing (3D-RADseq), resulting in a dataset of unparalleled resolution. Phylogenetic and structural analysis could distinguish four (I – IV) independent lineages. The strong population structure, low recombination and slow linkage decay strongly suggests that <em>C. lupini</em> reproduces clonally. Different morphologies and virulence patterns on white (<em>Lupinus albus</em>) and Andean lupin (<em>L. mutabilis</em>) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a mini-chromosome which was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this mini-chromosome could indicate a role in host interaction. All four lineages were present in the South American Andes region, which is concluded to be the center of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seed-borne pathogen, <em>C. lupini</em> has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.</p>
Microsatellite genotype data and leaf morphological data of the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence"
<p>These data sets were used for analyses in the publication "Bidirectional gene flow between <em>Fagus sylvatica</em> L. and<em> F. orientalis</em> Lipsky despite strong genetic divergence" accepted in Forest Ecology and Management <a href="https://www.sciencedirect.com/journal/forest-ecology-and-management/vol/537/suppl/C">Volume 537</a>, 1 June 2023, 120947, <a href="https://doi.org/10.1016/j.foreco.2023.120947">https://doi.org/10.1016/j.foreco.2023.120947</a></p> <p>For details about the data, please read the corresponding ReadMe files.</p>
Lepidoptera genomics based on 88 chromosomal reference sequences informs population genetic parameters for conservation
<p>This repository contains (1) germline mutations called by the DeepVariant (v1.1.0) pipeline in VCF format; (2) rejected substitution scores calculated by the Genomic Evolutionary Rate Profiling (GERP++) software on each species and chromosome; and (3) the phylogenetic tree used as guide tree in the Cactus alignment.</p>
Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates
<p>Sequence data and stepwise pipeline outputs associated with the article "Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates".</p> <p>Preprint available here: <a href="https://doi.org/10.22541/au.167085544.47638352/v1">10.22541/au.167085544.47638352/v1</a></p> <p>Sequence data is deposited in fastq-format in folders by region (Palinuro.tar.gz, Livorno.tar.gz, and Rovinj.tar.gz) and a separate folder for controls (Controls.tar.gz). Each fastq-file contains sequences for a single PCR replicate named by sample and replicate number. Sample names are described in spineless_sample_names.csv. Positive control sequences are described in SM1_positive_controls.csv. Stepwise pipeline outputs are available in the folder Pipeline_outputs_stepwise.zip</p> <p>Scripts used to generate pipeline outputs as well as other aspects of the final article are available at <a href="https://github.com/thomasdotter/spineless-haplotypes">https://github.com/thomasdotter/spineless-haplotypes</a>.</p> <p> </p>
Dataset of "Genetically-inspired convective heat transfer enhancement in a turbulent boundary layer"
<p>Dataset of the article "Genetically-inspired convective heat transfer enhancement in a turbulent boundary layer" (<a href="https://doi.org/10.1016/j.applthermaleng.2023.120621">https://doi.org/10.1016/j.applthermaleng.2023.120621</a>). The dataset contains:</p> <p>- the velocity fields, measured with Particle Image Velocimetry, for the case of the boundary layer without actuation, with actuation with a steady jet, and for the best individual obtained after the optimization of the pulsed jet parameters.</p> <p>- the parameters of the individuals generated in the optimization process.</p>
A Linked Application of Discrete Differential Evolution Algorithm Coupled with Simulation- Optimization Model and Comparative Analysis by Genetic Algorithm for Discrete Groundwater Management Problems
<p>Complete dataset of publication name as "The complete publication dataset is "A Discrete Differential Evolution- Linear Programming Algorithm for Groundwater Management Problems." You can find all the written codes in the zip file.</p>
Three systems of molecular markers reveal genetic differences between varieties sabina and balkanensis in the Juniperus sabina L. range
<p>Genotypes of 94 Juniperus sabina samples from 14 populations at SNP (Jsabina_SNPs.txt) and SilicoDArT (Jsabina_SilicoDArTs.txt) loci investigated using the DArTseq technology developed by Diversity Array Technology Pty Ltd (DArT, Canberra, ACT, Australia)</p>
Alliance of Genome Resources Genetic Interactions
<p>These files provide a set of annotations of genetic interactions for genes for human, rat, mouse, zebrafish, fruit fly, nematode, African clawed frog,and yeast). The files are in the <a href="https://github.com/HUPO-PSI/miTab/blob/master/PSI-MITAB27Format.md">PSI-MI TAB 2.7 format</a>, a tab-delimited format established by the <a href="http://www.psidev.info/">HUPO Proteomics Standards Initiative</a> Molecular Interactions (PSI-MI) working group. The interaction data are sourced from Alliance members WormBase and FlyBase, as well as the <a href="https://thebiogrid.org/">BioGRID database</a>. Identities or types of genetic perturbations for each interactor (if available) are provided in columns 26 and 27 and relevant phenotypes or traits (if available) are provided in column 28.</p> <ul> <li>Homo sapiens (human; NCBI:txid 9606)</li> <li>Caenorhabditis elegans (nematode; NCBI:txid 6239)</li> <li>Danio rerio (zebrafish;NCBI:txid 7955)</li> <li>Drosophila melanogaster (fruit fly; NCBI:txid 7227)</li> <li>Mus musculus (mouse; NCBI:txid10090)</li> <li>Rattus norvegicus (rat; NCBI:txid 10116)</li> <li>Saccharomyces cerevisiae (yeast; NCBI:txid 559292)</li> <li>Xenopus laevis (African clawed frog; NCBI:txid 8355)</li> </ul>
New Soil Metagenome-Assembled Genomes Catalogue Boosts Genetic Resources
<p><strong>Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conducted the first large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalog) from 3,304 soil metagenomes. We identified 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which greatly expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8,545 CRISPR-Cas genes. Additionally, we determined that uSGBs contributed 84.6% of novel viral-host associations identified from the SMAG catalog. Our results propose the SMAG catalog, a novel and expansive genomic resource that brings the soil microbial biodiversity and novel genetic resources to light.</strong></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.