Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
241
datasets available to search
ShareScore release 0.9.0
Dataset results
241 results for “Transcriber”
Fig. 2 in Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada)
Fig. 2 Phylogenetic tree topol- ogies and sampling locations. a Neighbor-joining tree obtained by ProfDistS and supporting bootstrap values (1,000 repli- cates) shown in black; CBC tree obtained by CBCanalyzer in dark grey; corresponding sampling locations indicated by arrows. b Numbers of CBCs distinguishing three species classified within Paramacrobiotus; grey ovals correspond to those in Fig. 2a and indicate the species groups that can be identified on the basis of CBCs
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75 in Integrative taxonomy of Parasabella and Sabellomma (Sabellidae: Annelida) from Australia: description of new species, indication of cryptic diversity, and translocation of some species out of their natural distribution range
Figure 3. Maximum likelihood topologies. A, cytochrome oxidase 1 fragments. B, internal transcribed spacer fragment. C, combined data set. Bootstrap supports over 75% shown on nodes. Scale bar, average of nucleotide substitutions per site.
Extensive intragenomic variation in the internal transcribed spacer (ITS) region of fungi
<p>Fungi are among the most biodiverse organisms in the world. Accurate species identification is imperative for studies on fungal ecology and evolution. The internal transcribed spacer (ITS) rDNA region has been widely accepted as the universal barcode for fungi. However, several recent studies have uncovered intragenomic sequence variation within the ITS in multiple fungal species. Here, we mined the genome of 2414 fungal species to determine the prevalence of intragenomic variation and found that the genomes of 641 species, about one-quarter of the 2414 species examined, contained multiple ITS copies. Of those 641 species, 419 (~65%) contained variation among copies revealing that intragenomic variation is common in fungi. We proceeded to show how these copies could result in the erroneous description of hundreds of fungal species and skew studies evaluating eDNA especially when making diversity estimates. Additionally, many genomes were found to be contaminated, especially those of unculturable fungi.</p>
Sequences of nuclear ribosomal internal transcribed spacer (ITS) for five Toxicodendron vernicifluum individuals
<p>This dataset includes the aligned sequences of nuclear ribosomal internal transcribed spacer (ITS) for five <em>Toxicodendron vernicifluum</em> individuals sampled from China.</p>
FIGURE 1. MrBayes phylogram inferred from incomplete internal transcribed spacer rDNA sequence data. Choiromyces meandriformis and C in A new species of Tuber (Tuberaceae, Pezizales) from Inner Mongolia, China
FIGURE 1. MrBayes phylogram inferred from incomplete internal transcribed spacer rDNA sequence data. Choiromyces meandriformis and C. alveolatus were used to root the tree. The same outcome was shown via Maximum Likelihood. On each branch, Bayesian posterior probability values (PP> 0.75) and maximum likelihood bootstrap values (MLbs> 75%) are displayed. The new species sequences are denoted by an asterisk (*). Different colours are used to represent the six primary Tuber phylogroups. Our findings establish T. mongolicum sp. nov. based on phylogenetic studies as well as morphological observations.
TRANSCRIBE (Transcriptomic Analysis of Left Ventricular Gene Expression)
ClinicalTrials.gov study NCT00985049. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Data from: Utility of internally transcribed spacer region of rDNA (ITS) and β-tubulin gene sequences to infer genetic diversity and migration patterns of Colletotrichum truncatum infecting Capsicum spp.
Open the record for dataset details and reuse information.
Data from: Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio
Open the record for dataset details and reuse information.
Extensive intragenomic variation in the internal transcribed spacer (ITS) region of fungi
Open the record for dataset details and reuse information.
nrDNA internal and external transcribed spacer sequences for investigating the systematics of Dieteria
Open the record for dataset details and reuse information.
Figure 4 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 4 Heatmap using Pearson's correlation coefficient between the OTUs generated from the ITS2 and LSU D1-D2 metabarcodes and the analysed beetle species and forest types. Rectangles indicate the strength of association between an OTU and beetle/forest (strongly negative, grey, to strongly positive, red). Fungal OTUs (on the horizontal axis) were classified to genus or species level where possible; they are shown in random order and cannot be linked taxonomically between both markers.
Supplementary material 1 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S1. Length distribution of the ITS (grey) and LSU (orange) OTUs
Figure 7 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 7 Closed reference clustering of OTUs and phylogenetic trees at different thresholds A results from the closed reference clustering of OTUs at each clustering threshold against composite LSU/ITS2 reference sequences. LSU matches in green, ITS2 matches in blue, linked matches (for which both an ITS2 and LSUOTU were matched to a reference sequence of the same species) in yellow. Underlined taxa indicate new matches at each clustering threshold B phylogenetic tree of LSUOTUs under increasingly stringent clustering thresholds, with arrows marking newly added taxa as threshold values are increased.
Figure 3 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 3 NMDS ordination plot of all specimens sampled with ITS2 and LSU D1-D2, based on the fungal community composition of the individual beetles. Shapes represent forest types and colours represent beetle species. Stress for this graph fell within acceptable ranges (<0.2).
Figure 2 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 2 Top panel: The proportion of OTUs identified as members of a fungal Class determined by the ITS2 and LSU D1-D2 regions. For the spruce forest, only nine X. germanus and four X. saxesenii specimens were retained after rarefaction. Lower panel: The number of fungal OTUs per beetle specimen, separate for each beetle species and forest type, for ITS2 and LSU.
Figure 6 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 6 Order-level trees and splitting/lumping of OTUs at clustering A order-level ML trees with mixed OTU clustering thresholds (99% LSU D1-D2, 98% ITS2). Full tree in supplementary materials. Leotia lubrica was used as the outgroup (not pictured). Brackets indicate reference taxa linked to an ITS2 and/or LSUOTU, with colours indicating potential splitting/lumping (blue, splitting; green, lumping; orange, 1:1) B diagram illustrating the effects of splitting and lumping of an OTU in the fungal community on the tree inference. Four hypothetical species (A to D) in a community are treated under uniform clustering thresholds for ITS2 and LSU. This may result in deviation from the 1:1 ratio of OTUs expected if each species in the community is represented equally by both markers (species A). Threshold values may be too high, resulting in splitting of species into multiples OTUs, which is likely to affect the more variable ITS2 region (species B) or may be too low, resulting in lumping of multiple species into a single OTU, likely to affect the conservative LSU region (species C and D).
Supplementary material 4 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S4. Binding site of ITS86 primer showing mismatched base pairs in Ophiostomatales
Figure 1 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 1 The proportion of fungi classified with IDTAXA, Protax-fungi and RDP from class to species level. "All" refers to the proportion of OTUs for which the three classifiers agreed in their classification.
Supplementary material 7 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Table S3. Number of OTUs assigned to each order based on RDP Bayesian classifier
Figure 5 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 5 ML tree of Sordariomycetes constructed from the reference sequence alignments and OTUs for both markers (clustering thresholds: 98% ITS2, 99% LSU D1-D2). Leotia lubrica (Leotiomycetes) was specified as the outgroup. The assignment of OTUs by each of the three classifiers (RDP, IDTAXA, Protax-fungi) is shown by coloured boxes. Terminals missing these boxes are the reference sequences. Coloured dots on the nodes of the tree indicate the hypothetical ancestor defining monophyletic groups corresponding to the various orders of Sordariomycetes. The extent of each order is indicated by the coloured inner ring. Note that the ancestor of an order is defined by the youngest node from which all reference sequences are descended; OTUs falling outside of the resulting clades appear as 'unassigned' by the phylogenetic analysis approach. The distribution of ITS2 (red squares) and LSU D1-D2 (blue bullets) relative to the reference set (yellow stars) on each of the tips of the tree. Note the limited presence of ITS sequences in the Ophiostomatales (in top right quadrant).
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.