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397 results for “Supplementary table”
Supplementary Table 11 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>Direct protein stable isotope fingerprinting (SIF) values for Kentron sp. H. δ<sup>13</sup>C values were offset-corrected using a human hair standard for each instrument run. Full raw and processed data are available from the PRIDE repository (https://www.ebi.ac.uk/pride/archive/) with the dataset identifier PXD011616.</p>
Supplementary Table 10 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>Number of genomes with each predicted metabolism in the IMG/ER database, based on the presence/absence of key genes. Except where noted, the number of genomes was not filtered for genome completeness.</p>
Supplementary Table 8 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>Hypothetical reaction scheme that can allow autotrophic CO<sub>2 </sub>fixation with enzymes that are predicted in Kentron genomes. Free energy values (Δ<sub>r</sub>G'<sup>m</sup>) were calculated for pH 7.0 and concentrations 1 mM using eQuilibrator (http://equilibrator.weizmann.ac.il)</p>
Supplementary Table 5 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>List of Transporter Classification families of energy-dependent organic substrate uptake transporters.</p>
Supplementary Table 6 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>Genomes of basal Gammaproteobacteria used for phylogenetic analysis and comparison of organic uptake transporter content. References are to genome description, if published, otherwise to author and date of data deposition. Taxonomy based on LPSN (http://www.bacterio.net), if available. Accession numbers are for INSDC contig sets or assemblies unless otherwise indicated.</p>
Supplementary Table 3 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>Key enzymes for autotrophic pathways, and enzymes of reference set used for comparison of read mapping vs SwissProt database.</p>
Supplementary Table 2 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>Summary statistics of Kentrongenome assemblies. Completeness, contamination, and strain heterogeneity values were estimated with conserved set of marker genes for Gammaproteobacteria using the CheckM pipeline.</p>
Supplementary Table 1 for "Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation"
<p>Collection localities and dates for <em>Kentrophoros </em>metagenomics and transcriptomics samples.</p>
Supplementary tables for "Theme Enrichment Analysis: A Statistical Test for Identifying Significantly Enriched Themes in a List of Stories with an Application to the Star Trek Television Franchise"
<p>Supplementary tables for the manuscript "Theme Enrichment Analysis: A Statistical Test for Identifying Significantly Enriched Themes in a List of Stories with an Application to the Star Trek Television Franchise".</p> <p>Supplementary Information File 1 contains a table of Star Trek TOS/TAS/TNG television series episodes featuring the Klingon alien race. The criterion for inclusion is that the Klingons were deemed by the authors to have been featured throughout the episode in a way that is central to the story plot.</p> <p>Supplementary Information File 2 contains tables of over-represented Literary Theme Ontology version 0.1.1 literary themes in Star Trek TOS/TAS/TNG television series storysets as identified by the hypergeometric test.</p> <p>Supplementary Information File 3 contains tables of over-represented Literary Theme Ontology version 0.1.1 literary themes in Star Trek TOS/TAS/TNG television series storysets as identified by the TF-IDF statistic.</p>
Supplementary tables S1-S5. Comparison of two different host plant genera responding to grapevine leafroll-associated virus 3 infection
<p>Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses of grapevine but, despite this, there remain several gaps in our understanding of its biology. Because of its narrow host range -limited to <em>Vitis</em> species - and because the virus is restricted to the phloem, most GLRaV-3 research has concentrated on epidemiology and the development of detection assays. The recent discovery that GLRaV-3 can infect <em>Nicotiana</em> <em>benthamiana, </em>a plant model organism, makes new opportunities available for research in this field. We used RNA-seq to compare both <em>V. vinifera </em>and <em>N. benthamiana</em> host responses to GLRaV-3 infection. This is the first analysis of gene expression profiles beyond <em>Vitis </em>to mealybug-transmitted GLRaV-3.</p>
Supplementary Tables for "A 3.3-Million-Year Record of Antarctic Iceberg Rafted Debris and Ice Sheet Evolution Quantified by Machine Learning"
<p>Supplementary Tables for "A 3.3-Million-Year Record of Antarctic Iceberg Rafted Debris and Ice Sheet Evolution Quantified by Machine Learning"</p> <p> </p> <p><strong>Table Captions:</strong></p> <p><strong>Table S1.</strong> Site U1537 Age Model Tie Points from Weber et al. (2022) and Reilly et al. (2021)</p> <p><strong>Table S2. </strong>Site U1537 Age Model used in this study, applying both the age tie points from Weber et al. (2022) and Reilly et al. (2021)</p> <p><strong>Table S3. </strong>Hole U1538A correlation to the Dove Basin Stack from Bailey et al. (2022), and the addition of the U1538 splice CCSF-A depth to the Dove Basin CCSF-A</p> <p><strong>Table S4. </strong>Site U1538 splice table used in this study, note the continuation down Hole A after Core 14H</p> <p><strong>Table S5. </strong>New top core section offsets for Site U1536 cores added to the Reilly et al. (2021) extended splice table</p> <p><strong>Table S6. </strong>New top core section offsets for Site U1537 cores added to Reilly et al. (2021) extended splice table</p> <p><strong>Table S7. </strong>Comparison of Convolutional Neural Network IRD counts to shipboard eye counts of IRD at Site U1536</p> <p><strong>Table S8. </strong>Site U1537 CNN IRD Counts per 50 cm bins</p> <p><strong>Table S9. </strong>Site U1536 IRD Fluxes Per 5 kyr Quantified by a Convolutional Neural Network (0-3.3 Ma)</p> <p><strong>Table S10. </strong>Site U1537 IRD Fluxes Per 5 kyr Quantified by a Convolutional Neural Network (0-3.3 Ma)</p> <p><strong>Table S11. </strong>Site U1536 IRD Fluxes Per 1 kyr Quantified by a Convolutional Neural Network (0-1.2 Ma)</p> <p><strong>Table S12. </strong>Site U1537 IRD Fluxes Per 1 kyr Quantified by a Convolutional Neural Network (0-1.2 Ma)</p> <p><strong>Table S13. </strong>Site U1538 IRD Fluxes Per 1 kyr Quantified by a Convolutional Neural Network (0-1.2 Ma)</p>
Sample metadata and supplementary tables for "Genomics identifies koala populations at risk across Eastern Australia"
<p>All metadata for the koala genomes deposited on NCBI under BioProject <span>PRJNA940526. Runs of homozygosity size classes and Gene Ontology terms provided as excel files.</span></p>
Supplementary tables for the paper: "Comprehensive Mapping of the AOP-Wiki Database: Identifying Biological and Disease Gaps"
<p><strong>Supplementary tables for the paper: "Comprehensive Mapping of the AOP-Wiki Database: Identifying Biological and Disease Gaps"</strong></p> <p><em>Original Research Article</em><br><strong>Frontiers in Toxicology</strong>, March 8, 2024<br>Section: Regulatory Toxicology<br><strong>Volume 6 - 2024</strong> | <a href="https://doi.org/10.3389/ftox.2024.1285768" target="_new" rel="noopener">https://doi.org/10.3389/ftox.2024.1285768</a></p> <p><strong>Authors</strong>:<br>Thomas Jaylet, Thibaut Coustillet, Nicola M. Smith, Barbara Viviani, Birgitte Lindeman, Lucia Vergauwen, Oddvar Myhre, Nurettin Yarar, Johanna M. Gostner, Pablo Monfort-Lanzas, Florence Jornod, Henrik Holbech, Xavier Coumoul, Dimosthenis A. Sarigiannis, Philipp Antczak, Anna Bal-Price, Ellen Fritsche, Eliska Kuchovska, Antonios K. Stratidakis, Robert Barouki, Min Ji Kim, Olivier Taboureau, Marcin W. Wojewodzic, Dries Knapen, Karine Audouze</p>
Supplementary Tables on Gene Annotations of 49 Bacillariophyta Genome Assemblies
<p>Supplementary Tables attaining to the manuscript entitled <strong>Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade. </strong>These Supplementary Tables describe in part the data foundation and results of the actual annotation dataset that is available at <a href="https://doi.org/10.5281/zenodo.13767023" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13767023</a>.</p> <p><strong>Supplementary Table S1</strong>: Genome assemblies available at NCBI Datasets in June 2024.</p> <p><strong>Supplementary Table S2</strong>: Genome assemblies excluded from annotation.</p> <p><strong>Supplementary Table S3</strong>: Accession numbers of genome assemblies and RNAseq libraries used for annotating 49 diatom genomes. Table also lists repeat content of genome assemblies after masking with RepeatModeler2/RepeatMasker.</p> <p><strong>Supplementary Table S4</strong>: Software and container versions used for annotating 49 diatom genomes.</p> <p><strong>Supplementary Table S5</strong>: Summary of EnTAP functional annotation results. The actual functional annotations are included in the annotation dataset that is available at <a href="https://doi.org/10.5281/zenodo.13767023" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13767023</a>.</p>
Supplementary Table S1. Combined analysis of variance containing the degrees of freedom (DF), mean squares (MS), P value (P val.), mean, coefficient of experimental variation (CEV%) and selective accuracy (SA) for the traits of luminosity (L*), chromaticity a* (a*), chromaticity b* (b*), grain length (length, mm), grain width (width, mm), grain thickness (thickness, mm), mass of 100 grains (Mass, g), normal grains (Ng, %), water absorption (absorption, %), cooking time (Ct, min:s), and concentrations of potassium (K, g kg-1 dry matter - DM), phosphorus (P, g kg-1 DM), calcium (Ca, g kg-1 DM), magnesium (Mg, g kg-1 DM), iron (Fe, mg kg-1 DM), zinc (Zn, mg kg-1 DM), and copper (Cu, mg kg-1 DM) obtained in 25 common bean cultivars evaluated in four experiments carried out from 2019 to 2021
<p><strong><span>Table S1.</span></strong><span> Combined analysis of variance.</span></p> <p><strong><span>Indirect selection for multiple technological and nutritional traits in common bean cultivars under different degrees of multicollinearity</span></strong></p> <p><strong><span>Bragantia, 2024.</span></strong></p>
Deliverable D1.4 - Supplementary material : Dataset on CS#2 Danube Suspect Screening Results Table : H2020 PROMISCES project
<p>Additional information on PROMISCES deliverable D1.4. Data set with list of substances identified in samples from the Danube catchment between Vienna and Budapest (CS#2) by suspect screening and database comparison and corresponding peak intensities. These data are non-target data, the measured intensities do not correspond to concentrations.</p>
Supplementary Table S2 - Stability of Blood DNA Methylation Across Two Timepoints in Three Cohorts
<p>Supplementary Table S2 from "Stability of Blood DNA Methylation Across Two Timepoints in Three Cohorts", published in Biomedicines.</p> <p><span>This research was funded by the National Science Centre, Poland, grant numbers 2017/26/E/NZ5/00851 (K.W.) and 2020/39/D/NZ5/02720 (J.K.N.).</span></p>
Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data
<p>Supplementary tables and figures - Excluding loci with substitution saturation improves inferences from phylogenomic data</p>
Genetic variation influencing DNA methylation provides new insights into the molecular pathways regulating genomic function - Selected Supplementary Tables
<p><strong>Selected Supplementary Tables - ST5, 7, 8 and 9</strong></p> <p><strong>Supplementary Table 5. Cosmopolitan results. </strong>Cosmopolitan SNP-CpG associations identified through genome-wide association amongst Europeans and South Asians.</p> <p><strong>Supplementary Table 7. Cross-tissue replication.</strong> Results for further testing of the 11,165,559 cosmopolitan SNP-CpG associations identified (by genome-wide association in blood), in 4 isolated white cell subsets (CD4+ lymphocytes, CD8+ lymphocytes, monocytes and neutrophils), in adipocytes isolated from subcutaneous adipose tissue or visceral adipose tissue, and in whole adipose tissue.</p> <p><strong>Supplementary Table 8. Conditional analysis.</strong> Results of conditional analysis to identify SNPs independently associated with each of the ~360K CpG sites tested. </p> <p><strong>Supplementary Table 9. Sentinel SNPs and CpGs.</strong> Results of R2 pruning and locus merging to identify discrete genetic and methylation loci that are associated, and their respective sentinel SNPs and sentinel CpG sites. </p> <p>Other files (e.g. annotation files and 'intermediate' processing files) referenced in our code are also provided. </p> <p> </p>
Fault trace data and supplementary table and figures of "Fault trace corrugation and segmentation as a measure of fault structural maturity"
<p>Fault trace data and supplementary information to the paper "Fault trace corrugation and segmentation as a measure of fault structural maturity" by Manighetti I., Mercier A., and de Barros L., Sept. 2021</p>
ScienceDex guides
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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.