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397 results for “Supplementary table”
Supplementary Table 1. Raw data of egg quality parameters for 990 egg samples with ATOL (Animal Trait Ontology for Livestock) descriptors, as function of hen age, pen no. and genotype in 15 replicates.
<p>Data table of egg quality parameters</p>
SUPPLEMENTARY TABLES: Defining the Sphagnum core microbiome across the North American continent reveals a central role for diazotrophic-methanotrophs in the nitrogen and carbon cycles of boreal peatland ecosystems
<p>Peat mosses of the genus <em>Sphagnum</em> are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. <em>Sphagnum</em> spp. host diverse microbial communities capable of nitrogen-fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic-methanotrophs represent a possible "missing link" between the carbon and nitrogen cycles, but the functional contributions of the <em>Sphagnum</em>-associated microbiome remain in question<em>.</em> A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate <em>Sphagnum</em> microbiome community composition across the North American continent and provide empirical evidence for diazotrophic-methanotrophy in <em>Sphagnum</em>-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 <em>Sphagnum</em> SSU rRNA libraries from peatlands across the US (5 states, 17 bog/fen sites, 18 <em>Sphagnum</em> species), with twelve genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (<em>nifH</em>) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by <em>Nostocales</em> cyanobacteria and <em>Rhizobiales</em> methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus <em>Methyloferula</em> (order <em>Rhizobiales</em>) accounted for one-quarter of transcribed <em>nifH</em> genes. Furthermore, in dual-isotope tracer experiments, members of the <em>Rhizobiales</em> showed substantial incorporation of <sup>13</sup>C-CH<sub>4</sub> and <sup>15</sup>N-N<sub>2</sub> isotopes into their rRNA. Our study characterizes the core <em>Sphagnum</em> microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (<em>Methyloferula</em> spp. of the <em>Rhizobiales</em>) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.</p>
Supplementary dataset and tables for "Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale"
<p><strong>Supplementary dataset and tables for "Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale"</strong></p> <p><strong>Supplementary Dataset and Tables</strong> listing identified acetone biosynthesis genes from mining of the DJ collection and gene and part sequences used for combinatorial library and cell-free prototyping (<strong>Supplementary Tab. 1</strong>), combinatorial library combinations and results (<strong>Supplementary Tab. 2</strong>), gene KO predictions (<strong>Supplementary Tab. 3</strong>), cell-free prototyping combinations and results (<strong>Supplementary Tab. 4</strong>), proteomics results for wild-type strain plus acetone biosynthesis plasmid (<strong>Supplementary Tab. 5</strong>), proteomics results for strain Δ<em>0553</em> plus select combinatorial library plasmids (<strong>Supplementary Tab. 6</strong>), Genbank accession numbers for 272 genomes (<strong>Supplementary Tab. 7</strong>). sequences of oligonucleotides (<strong>Supplementary Tab. 8</strong>) and emission factors used to calculate the GHG emissions of acetone (<strong>Supplementary Tab. 9</strong>) and IPA (<strong>Supplementary Tab. 10</strong>) in LCA.</p>
Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables
<p>Extreme <span>environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, </span><span>m</span><span>odern bony fishes have colonized various aquatic environments, including perpetually dark,</span><span> hypoxic, hypersaline and toxic habitats</span><span>. </span><span>Eurasian perch (</span><em>Perca fluviatilis</em><span>) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 SNPs, of which >10,000 were identified as potential candidates under selection (associated with >3,000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.</span></p>
Supplementary Table S5 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels
<p><strong>Table S5.</strong> Repository data showing genes identified by MapMan in Giza 178 in different pathways. </p> <p>A, Cell wall modifications.</p> <p>B, Hemicellulose synthesis.</p> <p>C, Cellulose synthesis.</p> <p>D, Mannan-xylose-arabinose-fucose. </p> <p>E, cell wall peroxidase.</p> <p>F, TF MYB. </p> <p>G, bZIP. </p> <p>H, Histone.</p>
Supplementary Table S4 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels
<p><strong>Table S4.</strong> Repository data showing genes identified by MapMan in Giza 177 in different pathways. </p> <p>A, Cell wall modifications.</p> <p>B, Hemicellulose synthesis.</p> <p>C, Cellulose synthesis.</p> <p>D, Mannan-xylose-arabinose-fucose.</p> <p>E, cell wall peroxidase.</p> <p>F, TF MYB. </p> <p>G, bZIP. </p> <p>H, Histone.</p>
Supplementary Table S2 - Article:Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels
<p><strong>Table S2.</strong> Repository data for the global analysis produced for cv Giza 177. </p> <p>A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls. </p> <p>B, Down regulated genes in Giza 177 observed when comparing salt stressed plants vs unstressed controls.</p> <p>C, Gene Ontology enrichment analysis (GOEA) results for Giza 177 up regulated genes. </p> <p>D, GOEA results for Giza 177 down regulated genes. </p>
Supplementary Table S3 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels
<p><strong>Table S3.</strong> Repository data for the global analysis produced for cv Giza 178. </p> <p>A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls. </p> <p>B, Down regulated genes in Giza 178 observed when comparing salt stressed plants vs unstressed controls.</p> <p>C, Gene Ontology enrichment analysis (GOEA) results for Giza 178 up regulated genes. </p> <p>D, GOEA results for Giza 178 down regulated genes. </p>
Supplementary tables for Honey Bee symbiont buffers larvae against nutritional stress and supplements lysine
<p>Honey bees have suffered dramatic losses in recent years, largely due to multiple stressors underpinned by poor nutrition. Nutritional stress especially harms larvae, who mature into workers unable to meet the needs of their colony. In this study, we characterize the metabolic capabilities of a honey bee larvae-associated bacterium, <em>Bombella apis</em> (formerly <em>Parasaccharibacter apium</em>), and its effects on the nutritional resilience of larvae. We found that <em>B. apis</em> is the only bacterium associated with larvae that can withstand the antimicrobial larval diet. Further, we found that <em>B. apis</em> can synthesize all essential amino acids and significantly alters the amino acid content of synthetic larval diet, largely by supplying the essential amino acid lysine. Analyses of gene gain/loss across the phylogeny suggest that four amino acid transporters were gained in recent <em>B. apis</em> ancestors. In addition, the transporter LysE is conserved across all sequenced strains of <em>B. apis</em>. Finally, we tested the impact of <em>B. apis</em> on developing honey bee larvae subjected to nutritional stress and found that larvae supplemented with <em>B. apis</em> are bolstered against mass reduction despite limited nutrition. Together, these data suggest a novel role of <em>B. apis</em> as a nutritional mutualist of honey bee larvae.</p>
Supplementary tables for the article "A novel approach for discovering correlations between elemental and molecular composition using laser-based spectroscopic techniques"
<p>Table S1. Collection conditions of zooplankton samples. Data in the salinity and temperature columns, separated by a slash sign, are the characteristics of surface and bottom water.</p> <p>Table S2. The results of elemental analysis of zooplankton by ICP-AES and ICP-MS (as provided by IO RAS).</p> <p>Table S3. List of emission signals used to construct spider diagrams.</p> <p>Table S4. List of spectral ranges eliminated from LIBS data to improve the performance of chemometric algorithms.</p> <p>Raw LIBS and Raman spectra of zooplankton.</p> <p> </p>
Supplementary Tables for the article"One-to-one Coupling between Southern Ocean Productivity and Antarctica Climate"
<p>Supplementary Tables for the article"One-to-one Coupling between Southern Ocean Productivity and Antarctica Climate".</p> <p>Table S1. Tie points in the age model of Site U1537; </p> <p>Table S2. Age-depth model and uncertainties at Site U1537;</p> <p>Table S3. Natural gamma radiation data at Site U1537;</p> <p>Table S4. Color reflectance component b* data at Site U1537;</p> <p>Table S5. Ca counts data at Site U1537;</p> <p>Table S6. Magnetic susceptibility data at Site U1537.</p>
Supplementary table of PRIDE datasets analyzed for "FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data"
<p>Our proteomics dataset comes from The PRoteomics IDEntifications (PRIDE) database, the world’s largest data repository of mass spectrometry-based proteomics data. Specifically, we used 633 human proteomics project experiments with a total of 32,546 runs and reanalyzed them using ionbot with an FDR threshold of 0.01 [16], resulting in a total of 154,885,151 peptide spectrum matches for 18,846 proteins. Here is the full list of projects, runs, and general statistics.</p>
Supplementary data of Figures (S1) and Tables (S1 & S2)
<p><strong>Figure S1. Comparison of early flower mutant recovered from irradiated PLBs at 10 Gy dose with the flower of ‘Emma White’ mother plant</strong></p> <p><strong>Table S1: Mean DNA intensity and nuclei count of gamma irradiated PLBs after five months of irradiation treatment</strong></p> <p><strong>Table S2: RAPD primers used for genetic study of gamma irradiated mutants</strong></p>
Supplementary Tables 1 and 2
<p><strong><span>Acute Pancreatitis in Pediatric Acute Lymphoblastic Leukemia (AcuPA Study). A Nationwide Survey in Poland. </span></strong></p> <p>Supplementary Tables 1 and 2 </p>
Supplementary Tables
Open the record for dataset details and reuse information.
Supplementary Tables
<p>Supplementary Tables accompaniying the following manuscript:</p> <p>Adeoye et al. <strong><em>Systematic Analysis of Biological Processes Reveals Gene Co-expression Modules Driving Pathway Dysregulation in Alzheimer’s Diseas</em>e </strong><em>bioRxiv : the preprint server for biology</em> 2024.03.15.585267. 15 Mar. 2024, doi:10.1101/2024.03.15.585267. Preprint.</p> <p>A brief description of the file contents is as follows:</p> <p><strong>Supplementary Table 1.</strong> Sample metadata for all 20 donors, including post-mortem neuropathological assessments, clinical evaluations, and pathological grouping.</p> <p><strong>Supplementary Tables 2—4.</strong> The table of p-values and log fold changes for all genes included in the differential analysis test across all brain regions (MTG 2; STG 3; ETC 4) and cell types.</p> <p><strong>Supplementary Table 5. </strong>Table of pathway renaming conventions.</p> <p><strong>Supplementary Tables 6—8.</strong> Comprehensive documentation of the pathway analysis results for each brain region (MTG 6; SFG 7; ETC 8) with detailed statistical results (coefficient estimates and p-values) for the prioritized candidate pathways identified across major cell types. </p> <p><strong>Supplementary Tables 9—11.</strong> Results from DME analysis for each brain region (MTG 9; SFG 10; ETC 11) across all cell types.</p> <p><strong>Supplementary Table 12.</strong> List of overlapping dysregulated pathways along with corresponding statistics for each cell type.</p> <p><strong>Supplementary Table 13.</strong> List of hub genes and hDEGs in each module for all cell types across brain regions.</p> <p>Overlapping hub genes are presented in <strong>Supplementary Table 14</strong>.</p>
The Category-Modifier system: a hierarchical classification scheme for vertebrate tooth marks - supplementary tables
<p>Preserved records of tooth-bone interactions, known as tooth marks, can yield a wealth of information regarding organismal behavior and ecology. For this reason, workers in a wide range of disciplines, but particularly paleontology, have inspected and interpreted these features for decades. Although previous studies have gleaned invaluable insights, they have also described tooth marks using terminological frameworks that have been incompletely defined, have incorporated behavioral hypotheses in definitions, and/or have been inconsistently applied. To address these problems, we introduce the Category-Modifier (CM) system, the first system to both sort tooth marks into clearly defined main categories and use descriptive modifiers to characterize their appearance more precisely. The CM system is designed to apply to a wide range of vertebrates, to enable comparisons across disciplines and studies, and to help researchers keep their investigations into behavioral hypotheses free of circular reasoning.</p>
Additional Supplementary Tables for PTMNavigator Manuscript
<p>Additional supplementary tables that did not fit into the initial submission</p>
Supplementary Table 7b
<p>Gene ontology enrichment analysis based on genes for each expression pattern observed among CeD, FDR and Control</p>
Supplementary Table 5c
<p>Reactome pathway enrichment for down in FDR based on adjusted-pvalue <= 0.05 and without log2(FC) criteria</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.