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348
datasets available to search
ShareScore release 0.9.0
Dataset results
348 results for “Core data”
Data from: Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly
A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.
Data from: Global pairwise RNA interaction landscapes reveal core features of protein recognition
RNA–protein interactions permeate biology. Transcription, translation, and splicing all hinge on the recognition of structured RNA elements by RNA-binding proteins. Models of RNA–protein interactions are generally limited to short linear motifs and structures because of the vast sequence sampling required to access longer elements. Here, we develop an integrated approach that calculates global pairwise interaction scores from in vitro selection and high-throughput sequencing. We examine four RNA-binding proteins of phage, viral, and human origin. Our approach reveals regulatory motifs, discriminates between regulated and non-regulated RNAs within their native genomic context, and correctly predicts the consequence of mutational events on binding activity. We design binding elements that improve binding activity in cells and infer mutational pathways that reveal permissive versus disruptive evolutionary trajectories between regulated motifs. These coupling landscapes are broadly applicable for the discovery and characterization of protein–RNA recognition at single nucleotide resolution.
Mont Blanc ice core data for NH3 source investigation in Europe
<p>Dataset to interpret the <i>δ</i>15N(NH4+) in a Mont Blanc ice core</p>
GZF251 core data
<p>Grain size, magnetic parameters and related data.</p>
Data and codes: Automated estimation of bioturbation intensity and ichnodiversity from the core section image using convolutional neural network
Open the record for dataset details and reuse information.
Grain size, color reflectance and magnetic susceptibility data from core DY-1 in the Datong Basin, north China
<p>Linear-interpolation time scale for the series are added for consideration</p>
Phenotypic data for the Sorghum bicolor core collection selected from the whole collection in the Uganda National GeneBank
<p>Passport data for the Sorghum bicolor core collection selected from the whole collection in the Uganda National GeneBank (Information is based on 286 core collection accessions, excluding 24 accessions which did not germinate in this trial</p>
Supplementary material 2 from: Woodburn M, Buschbom J, Droege G, Grant S, Groom Q, Jones J, Trekels M, Vincent S, Webbink K (2022) Latimer Core: A new data standard for collection descriptions. Biodiversity Information Science and Standards 6: e91159. https://doi.org/10.3897/biss.6.91159
Standards with LtC alignments
Supplementary material 1 from: Woodburn M, Buschbom J, Droege G, Grant S, Groom Q, Jones J, Trekels M, Vincent S, Webbink K (2022) Latimer Core: A new data standard for collection descriptions. Biodiversity Information Science and Standards 6: e91159. https://doi.org/10.3897/biss.6.91159
A summary of the classes in the Latimer Core standard.
iGEM-Leiden-2022-Core Experiments 6 Raw Absorbance Data
<p>Raw absorbance data Core Experiment 6 iGEM Leiden 2022</p>
iGEM-Leiden-2022-Core Experiments 4 Formatted Absorbance Data
<p>Formatted absorbance data Core Experiment 4 iGEM Leiden 2022</p>
iGEM-Leiden-2022-Core Experiments 3 Raw Absorbance Data
<p>Raw absorbance data Core Experiment 3 iGEM Leiden 2022</p>
iGEM-Leiden-2022-Core Experiments 2 Formatted Absorbance Data
<p>Formatted absorbance data Core Experiment 2 iGEM Leiden 2022</p>
iGEM-Leiden-2022-Core Experiments 1 Raw Absorbance Data
<p>Raw absorbance data Core Experiment 1 iGEM Leiden 2022</p>
iGEM-Leiden-2022-Core Experiments 5 Raw Absorbance Data
<p>Raw absorbance data Core Experiment 5 iGEM Leiden 2022</p>
Core-Alkynylated Fluorescent Flippers: Altered Ultrafast Photophysics to Track Thick Membranes: Original Data
<p>Original data</p>
Data for the paper "Using Extensive Core-reflected Phases to Constrain Sharp Inner Core Boundary beneath East Asia"
Open the record for dataset details and reuse information.
Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.
Figure 3 from: Remsen D, Knapp S, Georgiev T, Stoev P, Penev L (2012) From text to structured data: Converting a word-processed floristic checklist into Darwin Core Archive format. PhytoKeys 9: 1-13. https://doi.org/10.3897/phytokeys.9.2770
Figure 3 - An updated database with final column titles and unique identifier added for each record.
Data from: The first high-resolution aerosol pH change since industrial revolution constructed by the nitrogen isotopes of ice core ammonium
<p><span><span>Aerosol acidity has broad significance in the atmosphere and ecosystems; however, a reliable way to quantify its changes over long time is lacking. Here, we propose a n</span><span>ew</span><span> approach calculating aerosol pH based on the nitrogen stable isotope composition (δ15N) of aerosol ammonium (NH4+) and for the first time reconstruct historical trajectory of aerosol pH over the last two centuries via δ15N of NH4+ achieved in a Tibetan ice core. We observed a significant decrease in δ15N of ice core NH4+ by 13‰ from the preindustrial to modern era, corresponding to a decreased in aerosol pH by 0.75 units. The decline in pH demonstrates a dominant role of anthropogenic emissions in acid gases over alkaline gases since Industrial Revolution. Our study also suggests that spatiotemporal patterns of aerosol acidity could be widely revealed by future nitrogen stable isotope of aerosol</span><span> or ice core</span><span> ammonium measurement, which in turn will promote the understanding in aerosol chemistry in the context of global environmental changes.</span>y in the context of global environmental changes.</span></p>
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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.