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2,848 results for “sequence data”
Complementary sequence and model data for fungal E3BP
<p>Multiple Sequance Alignments (MSA) and atomic models of E3BP predicted using AlphaFold (AF), as supplementary datasets to the publication "The structure and evolutionary diversity of the fungal E3-binding protein" (2023)</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.
R notebooks to reproduce all analyses from the manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis"
<p>This package contains all R notebooks to reproduce the analyses from our manuscript "grandR: a comprehensive package for nucleotide conversion sequencing data analysis".</p> <p>In the zip file you find</p> <ul> <li>several rds files in the data folder: They contain grandR objects of both simulated and real SLAM-seq data sets. You can delete them and create them again by either just "knitting" the notebooks (which will generate all data necessary for this notebook and save it into the data folder), or by executing the generateAllDataFiles.R script ("Rscript generateAllDataFiles.R"), which will generate all rds files that do not exist).</li> <li>several R notebooks (Rmd): "Knitting" them will generate all figures from the manuscript. Without the data files (rds), this will be slow!</li> <li>knit_all.bash: Execute to "knit" all notebooks</li> <li>clean.bash: Clear the output of "knitting" the notebooks</li> </ul> <p> </p>
Complete organelle genomes of Korean fir, Abies koreana and phylogenomics of the gymnosperm genus Abies using nuclear and cytoplasmic DNA sequence data
<span>Background</span> <p><em><span>Abies koreana</span></em><span> E. H. Wilson is an endangered evergreen coniferous tree that is native to high altitudes in South Korea and susceptible to the effects of climate change. Hybridization and reticulate evolution have been reported in the genus; therefore, multigene datasets from nuclear and cytoplasmic genomes are needed to better understand its evolutionary history.</span></p> <span>Results</span> <p><span>Using Illumina NovaSeq6000 and Oxford Nanopore Technologies (ONT) PromethION platforms, we generated complete mitochondrial (1,174,803 bp) and plastid (121,341 bp) genomes from <em>A. koreana</em>. The mitochondrial genome is highly dynamic, transitioning from cis- to trans-splicing and breaking the conserved gene clusters. In the case of the plastome, the ONT reads revealed two structural conformations of <em>A. koreana</em>. The short inverted repeats (1,186 bp) of the <em>A. koreana</em> plastome are associated with the different structural types. Transcriptomic sequencing revealed 1,356 sites of C-to-U RNA editing in the 41 mitochondrial genes. Using <em>A. koreana</em> as a reference, we additionally produced nuclear ribosomal DNA and organelle genomic sequences from eight Abies species and generated multiple datasets for maximum likelihood and network analyses. Three sections (<em>Balsamea</em>, <em>Momi</em>, and <em>Pseudopicea</em>) were well grouped in the nuclear phylogeny, but the phylogenomic relationships showed conflicting signals in the mitochondrial and plastid genomes, indicating a complicated evolutionary history that may have included introgressive hybridization.</span></p> <span>Conclusions</span> <p><span>These results illustrate that phylogenomic analyses based on the sequences from differently inherited organelle genomes resulted in conflicting trees. Organellar capture, organellar genome recombination, and incomplete lineage sorting in an ancestral heteroplasmic individual can contribute to phylogenomic discordance. We provide strong support for the relationships within <em>Abies</em> and new insights into the phylogenomic complexity of this genus.</span></p>
Genome Alignment of Cancer Sequencing Data
<p>Part of the GTN Cancer Analysis learning Pathway based on the Bioinformatics.ca Cancer Workshop</p>
FIG. 2 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data
FIG. 2. Strict consensus tree of the 30,000 most parsimonious trees based on the combined trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 1 (not weighted) including 58 taxa; Length = 524, CI = 0.479, RI = 0.601, RC = 0.288. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.
FIG. 1 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data
FIG. 1. Strict consensus tree of the 30,000 most parsimonious trees based on the 5S spacer sequence data recoverd during heuristic Search 3 for 56 taxa; Length = 231, CI = 0.519, RI = 0.743, RC = 0.386. Values above the internodes give the jackknife values (where absent, the jackknife values are less than 50%). Members of the Lampranthus group are underlined.
FIG. 3 in A Molecular Systematic Study of the Lampranthus Group (Aizoaceae) Based on the Chloroplast TrnL-trnF and Nuclear ITS and 5S NTS Sequence Data
FIG. 3. Strict consensus tree of the 167 most parsimonious trees based on the combined and successively weighted trnL-F, ITS and 5S spacer sequence data recovered during simultaneous analysis 4 including 51 taxa; CI = 0.599, RI = 0.841, RC = 0.504. Values above the internodes give the jackknife values. Members of the Lampranthus group are underlined.
Generated sequences and fitness data for ProGen2
<p>Sequences generated from pretrained and fine-tuned ProGen2 models. Fitness benchmark data for evaluation of ProGen2 models.</p>
Sequencing data from validation experiment for base editing of SCN2A
<p>It is challenging to apply traditional mutational scanning to voltage-gated sodium channels (NaVs) and functionally annotate the large number of coding variants in these genes. Using a cytosine base editor and a pooled viability assay, we screened a library of 368 guide RNAs (gRNA) tiling NaV1.2 to identify more than 100 gRNAs that changed NaV1.2 function. We sequenced base edits made by a subset of these gRNAs to confirm specific variants that drove changes in channel function. Electrophysiological characterization of these channel variants validated the screen results and provided functional mechanisms of channel perturbation. The majority of the changes caused by these gRNAs were classified as loss-of-function along with two missense mutations that led to gain-of-function in NaV1.2 channels. This two-tiered strategy to functionally characterize ion channel protein variants at scale identifies the largest set of loss-of-function mutations in a single NaV1.2 study to date.</p>
FIGURE 39 Modica confusa comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 39 Modica confusa comb.n. (a–d) male genitalia (dissection KW-21-64), lateral (a) with posterior view juxta, dorsal (b), aedeagus lateral (c) and aedeagus dorsal (d); (e–h) female genitalia (dissection KW-21-65), lateral view exterior tip abdomen (e), ventral view exterior tip abdomen (f), dorsal view interior abdomen (g), corpus bursae perpendicular to signa (h). Scale bars 1 mm.
FIGURE 36 Deltaya gen.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 36 Deltaya gen.n. Species diversity mapped on a 2 degree grid. Colours ranging from dark green to red represent increasing diversity.
FIGURE 33 Deltaya ocypete comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 33 Deltaya ocypete comb.n. (a) male wing venation; (b and c) male (FLMNH-MGCL-209681) dorsal (b) and ventral (c); (d and e) female dorsal (d) and ventral (e). Scale bars 1 cm.
FIGURE 30 Occulta ocnus comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 30 Occulta ocnus comb.n. (a) male wing venation; (b and c) male (LEP-10408) dorsal (b) and ventral (c); (d and e) female (ST ocnus) dorsal (d) and ventral (e), with specimen labels. Scale bars 1 cm.
FIGURE 35 Deltaya ocypete comb.n. A-E in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 35 Deltaya ocypete comb.n. A-E, male genitalia (dissection KW-21-66), lateral (a) with posterior view juxta, dorsal (b), aedeagus lateral (c) and aedeagus dorsal (d), vesica everted showing cornuti (e); (f–i) female genitalia (dissection KW-21-67), lateral view exterior tip abdomen with 8th segment retracted (f), lateral view exterior tip abdomen with 8th segment extended (g), ventral view exterior tip abdomen (h), dorsal view interior abdomen (i). Scale bars 1 mm.
FIGURE 31 Occulta ocnus comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 31 Occulta ocnus comb.n. (a and b) male genitalia (dissection SN-19-157), lateral (a) with posterior view juxta, aedeagus lateral (b); (c–e) female genitalia (dissection NHMUK010402850), lateral view exterior tip abdomen (c), ventral view exterior tip abdomen (d), dorsal view interior abdomen (e), corpus bursae perpendicular to signa (f). Scale bars 1 mm.
FIGURE 27 Trico tricolor fulgoracomb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 27 Trico tricolor fulgoracomb.n. (a and b) male dorsal (a) and ventral (b); (c and d) female dorsal (c) and ventral (d). Scale bars 1 cm.
FIGURE 23 Xenovena murryae comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 23 Xenovena murryae comb.n. (a) male wing venation; (b and c) male dorsal (b) and ventral (c); (d and e) female dorsal (d) and ventral (e). Scale bars 1 cm.
FIGURE 19 Argentaria itonis comb.n. A-E in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 19 Argentaria itonis comb.n. A-E, male genitalia (dissection KW-21-41), lateral tip abdomen (a), lateral (b) with posterior view juxta, dorsal (c), aedeagus lateral (d) and aedeagus dorsal (e); (f–i), female genitalia (dissection KW-21-60), lateral view exterior tip abdomen (f), ventral view exterior tip abdomen (g), dorsal view interior abdomen (h), corpus bursae perpendicular to signa (i). Scale bars 1 mm.
FIGURE 21 Taguaiba drogoni comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)
FIGURE 21 Taguaiba drogoni comb.n. (a) male wing venation; (b and c) male dorsal (b) and ventral (c); (d and e) female dorsal (d) and ventral (e). Scale bars 1 cm.
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.