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1,773 results for “Supplementary data,”
Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity - Supplementary Data - ANALYSES - Data S3
<p>Macroalgae are a polyphyletic group of multicellular aquatic organisms vital to global climate maintenance and have a wide variety of commercial applications. The lack of genomic datasets and poor physiological records preclude understanding their ecological roles and industrial potential. We <em>de novo</em> sequenced 121 macroalgal genomes from various climates spanning five major latitude parallels. The resultant genomic datasets reveal genetic bases for niche habitation facilitated by morphological complexity in diverse and extreme regions and illuminate the evolutionary mechanisms behind macroalgal diversification and specialization. Adhesome genes (e.g., cadherins, integrins, and lectins), extracellular matrix enzymes, and cytoskeletal organization regulating genes (e.g., spondins, Rho-type GTPases) predominantly distinguished macroalgal genomes from their microalgae correlates. Deep neural networks could accurately classify an alga as micro- or macro- from set of significance-ranked genomic features (n = 251, entropy R<sup>2</sup> > 0.99, RASE = 0.001) as well as adhesome gene sets (n = 110, entropy R<sup>2</sup> > 0.86). By deciphering the macroalgal adhesome, a clear picture of the genetic basis for the development and maintenance of complex algal tissues could be resolved. Sequences from giant viruses were rampant in the macroalgal genomes and coded for zinc-finger transcription factors, ankyrins, Rieske proteins, and other exotic codomains. Lineage-specific retentions of transcription factors, cadherins, integrins, polysaccharide-acting enzymes, and receptor kinases, many with predicted viral origins, outline the divergent mechanisms facilitating multicellularity in these three macroalgal lineages. This work sheds new light on the evolution of multicellularity in three phyla (Rhodophyceae, Chlorophyceae, and Ochrophyceae v. Phaeophyceae) through the lens of large-scale genomics and paves the way for the genomic exploration of macroalgal biology.</p> <p> </p> <p><strong>Data S3.</strong> <strong>Analysis data files.</strong> This dataset includes data files for the analyses presented in the manuscript, including</p> <p>(A) Decontamination analysis, including iterative BLEACH contamination calls, GFF coordinates for contaminants, and downsampling analyses of decontaminated genomes. Related to Fig. S1.</p> <p>(B) HMMsearch results for decontaminated assemblies for PFAMs. Related to Figs. 2-6.</p> <p>(C) Ternary analyses including dcGO enrichment for >80% purity sets for the three phyla. Related to Fig. 2.</p> <p>(D) Comparative genomics analyses of micro- and macroalgal genomes, including intersection, response screening, metabolic pathway, GO enrichment, and aNN modeling analyses. Related to Fig. 3.</p> <p>(E) Adhesome analysis including HMMsearch results for adhesome domains and codomains and response screening analyses between phyla, habitat, climate, and micro- vs. macroalgae. The neural network model using the 110 adhesome PFAMs is also included in this dataset. Related to Fig. 4.</p> <p>(F) Endogenous viral element analyses, including VFAM HMMsearch results, EVOPs, macroalgal sequences with EsV-1-7 codomains and comparative analyses including response screens and hierarchical clustering results. Related to Fig. 5.</p> <p>(G) All computational scripts used for analyses in this study. Scripts are either ‘.sh’ or ‘.sbatch’ files for execultion in a Linux environment with a SLURM (<a href="https://github.com/SchedMD/slurm">https://github.com/SchedMD/slurm</a>) high-performance computing (HPC) scheduler. Related to all analyses.</p>
Supplementary materials for: Actually accessible data: An update and a call to action
<p>These are the supplementary materials for the article "Actually Accessible Data: An Update and a Call to Action." The project contains three files:</p> <ol> <li>Colon-Karcher-Goben_Accessibility-of-Popular-Data-Repositories.xlsx shows the results of automated accessibility checks of seven popular data repositories in the United States and Europe. For each repository a search or browse page as well as a typical dataset landing page were selected and checked with two prominent accessibility tools AXE (https://www.deque.com/axe/) and WAVE (https://wave.webaim.org/). Checks were initially performed in Spring 2022. The reported (mostly unchanged) results are from tests on April 25, 2023. They were performed using Firefox 112.0.2 for Windows with both browser add-ons installed, AXE v. 4.6.3, WAVE v. 3.2.</li> <li>Colon-Goben-Karcher_Acessibility-FLOSS-Repositories.xlsx describes the treatment of digital accessibility in the developer-oriented documentation of six popular open-source (data) repository software projects. The project documentation was reviewed by two researchers with a background in open source software (Karcher as well as a graduate assistant at the Qualitative Data Repository) who looked for specific sections on accessibility and also used search terms to identify relevant sections. This document reflects the status as of April 2022.</li> <li>Colon-Goben-Karcher_Search-Strategies.docx Briefly discusses the literature search strategies conducted for relevant literature. Initial searches in Google Scholar and Scopus were performed in March-April 2022. Additional searches in LISTA are from March-April 2023.</li> </ol>
curatedPCaData supplementary data table for differential gene expression analysis
<p>This tab-separated plaintext file contains differential gene expression analyses reported for the curatedPCaData data resource publication.</p>
Data and Supplementary Plots for A Shallow Water Model Exploration of Atmospheric Circulation on Sub-Neptunes
<p>This repository contains geopotential maps, zonal wind plots, gifs, and data for the ensemble of possible sub-Neptunes presented in the main manuscript. The data, individual plots, and plot grids are based on the averages of the last 100 simulated days. The data are in the pickle format (see https://docs.python.org/3/library/pickle.html)<br> The gifs are based on the last 1000 simulated hours. These figures and gifs support the analysis presented in the main manuscript.</p>
Supplementary data for the study "Unveiling the rheological control of magmatic systems on volcano deformation: the interplay of poroviscoelastic magma-mush and thermo-viscoelastic crust ", submitted in the Journal of Geophysical Research: Solid Earth
<p>Supplementary data for the study "Unveiling the rheological control of magmatic systems on volcano deformation: the interplay of poroviscoelastic magma-mush and thermo-viscoelastic crust ", submitted in the Journal of Geophysical Research: Solid Earth</p>
Supplementary data for "Genomic signatures of strawberry domestication and breeding" paper
<pre>############################################################################################ ## Supplementary data for "Genomic signatures of strawberry domestication and breeding" ## ## Author: Zhen Fan ## ## Date: 6/26/2023 ## ############################################################################################</pre> <p>Octoploid strawberry SNP map (SNP.vcf.gz) includes filtered SNP using 289 individuals.</p> <p>GWAS_raw.zip includes raw data, BLUE estimates, genotyping data and marker positions for GWAS study of fruit size and yield. </p>
Supplementary files for "Data-driven estimation of nitric oxide emissions from global soils based on dominant vegetation covers"
<p>In-situ observations collected from publications, data-driven model codes, DNDC simulation files, and the supporting data for all figures of this study are uploaded. In-situ observations included 1,356 observations of soil nitric oxide (NO) emissions from 192 sites, including 1,032 for cropland soils from 70 sites, 114 for grassland soils from 36 sites, and 208 for forest soils from 86 sites. Data-driven models provided three machine learning methods, including random forest (RF), generalized boosted regression model (GBM), and radial basis function (RBF). The DNDC simulation files included simulation files of 51 selected sites.</p>
Supplementary Data for "Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates"
<p>Supplementary data includes original sample names and locations, raw geochemical and granulometric data, and calculated geochemical data represented as figures for the manuscript titled "<strong>Assessing weathering, pedogenesis, and silt generation in granitoid-hosted soils from contrasting hydroclimates"</strong>. All datasets are in the same excel file on separate tabs. All data were processed according to established procedures cited in the manuscript text. All software used is open access: ImageJ, adobe illustrator, and Microsoft excel.</p>
Supplementary data for "Coral connectivity and resilience in the southwest Indian Ocean"
<p>Supplementary data (including scripts and figures) for <em>Coral connectivity and resilience in the southwest Indian Ocean</em> in <em>Marine dispersal in the western Indian Ocean</em>.</p>
StrainIQ software mamuscript- Supplementary data
<p>This is supplemental material presented in the study, "StrainIQ: A novel <em>n</em>-gram based method for taxonomic profiling of human microbiota at the strain-level".</p> <p>Please find the new link for this data at https://zenodo.org/record/8132164</p>
Volatile traps as a new supplementary method of light trap for assessing diversity and composition of Macroheterocera assemblages - RAW Data
<p>Volatile traps as a new supplementary method of light trap for assessing diversity and composition of Macroheterocera assemblages - RAW Data</p>
Supplementary Data and Results Files for Heggarty et al. (2023) in Science, https://doi.org/10.1126/science.abg0818
<p>The supplementary data and results files for a Bayesian phylogenetic analysis of the Indo-European language family, published as Heggarty et al. (2023) in Science, https://doi.org/10.1126/science.abg0818.</p> <p> </p> <p> </p>
Supplementary data for Contribution of reproductive developmental gene diversity to the morphological variability of panicle in African rice
<p> </p> <p>African rice, <em>Oryza glaberrima</em> Steud., is a crop closely related to Asian rice (Oryza sativa L.) and represents a valuable resource for enhancing biotic and abiotic resistance properties in rice cultivation. Despite extensive research on the genetic basis of panicle architecture in O. sativa, our understanding of the molecular genetic factors governing this essential trait in <em>O. glaberrima</em> remains limited. Furthermore, there is a significant knowledge gap regarding the intra- and inter-specific diversity of panicle development and architecture in relation to the domestication of rice species. To bridge these gaps, our study employed a comprehensive approach, including in silico analyses, candidate gene-based association analysis, genome-wide association analysis, and analysis of structural variants (SVs) present in GWAS sites. The findings of this study significantly contribute to our understanding of the molecular genetic factors underlying rice panicle development and architecture. Furthermore, they provide promising targets for future efforts to improve the panicle morphological traits of this essential crop.</p>
Supplementary Data Tables for 'The Global Drivers of Chronic Coastal Flood Hazards under Sea-Level Rise'
<p>Please refer to and cite the manuscript Hague et al. (2023), 'The Global Drivers of Chronic Coastal Flood Hazards under Sea-Level Rise', Earth's Future. https://doi.org/10.1029/2023EF003784 </p> <p> </p>
Supplementary data to "What are the effects of temperature on plasticity, shape symmetry and seasonal variation in freshwater benthic green microalga Micrasterias thomasiana?"
<p>The supplementary data consist of the files including the landmark coordinates of Micrasterias thomasiana semicells used for the analyses described in the manuscript submitted to Aquatic Ecology. The coordinates are presented in the TPS format.</p> <p> </p>
BP-tracer: Supplementary Data 2
<p><strong>Supplementary Data 2 of BP-tracer</strong></p> <p>Including:</p> <p>1. BP-Tracer analysis results of simulated metagenomes </p> <p>2. BP-Tracer analysis results of real metagenomes</p>
Supplementary data for "Nanostructure explains the behavior of slippery covalently-attached liquid surfaces"
<p>Slippery covalently-attached liquid surfaces (SCALS) with low contact angle hysteresis (CAH, <5˚) and nanoscale thickness display impressive anti-adhesive properties, similar to lubricant-infused surfaces.<br> Their efficacy is generally attributed to the liquid-like mobility of the constituent tethered chains. However, the precise physico-chemical properties that facilitate this mobility are unknown, hindering rational design. This work quantifies the chain length, grafting density, and microviscosity of a range of polydimethylsiloxane (PDMS) SCALS, elucidating the nanostructure responsible for their properties.</p> <p>Zip files of neutron reflectometry and single-molecule force spectroscopy data are included here.</p>
Supplementary Data for "Co-occurrence of climate-change induced and anthropogenic pressures in Central American key biodiversity areas"
<p>Supplementary Data for the article "Co-occurrence of climate-change induced and anthropogenic pressures in Central American key biodiversity areas"</p> <p>This includes the pressure score maps for all climate scenarios / SSPs for the historical and future time periods as well as the script used for preparing the anthropogenic pressure maps (human footprint mapping).</p>
Supplementary data for "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism."
<p>This page contains public data for the peer-reviewed publication:<br> Matthew B. Goss and Jesse H. Kroll: "Chamber studies of OH + dimethyl sulfoxide and dimethyl disulfide: insights into the dimethyl sulfide oxidation mechanism." ACP, XX, XXXX–XXXX, 202X. Submitted.</p> <p>These data files are intended as additional supplementary information for this publication. If you would like to use any data herein in a publication, please contact the corresponding author (Matthew Goss, mgoss@mit.edu) first.</p> <p>Data files contain product concentration timeseries. Time is reported in seconds after UV lights were turned on. All data, except for ozone and NOx timeseries, have been corrected for chamber dilution. Product concentrations are reported in parts per billion.</p> <p>If you have any more questions, please contact the corresponding author, Matthew Goss at mgoss@mit.edu.</p>
Supplementary data to translate ages across humans and great apes
<p>We have generated a large dataset consisting of 573 time points from various behavioral, anatomical, and transcriptional changes across human and eight non-human primate species. This dataset includes diverse human populations to capture within-species variations. We aligned ages across humans and great apes across their lifespan. Our findings indicate that human lifespan is unusually extended lifespan compared to other primates, suggesting a unique phase of life without a clear counterpart in great apes.</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.