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19,342 results for “Sequences”
Data from: Genome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis
<p>The genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.</p>
Plasmid sequence of cpX
<p>Sequence of plasmid </p>
Fig. 1 in Emendation of the Genus Auritidibacter Yassin et al. 2011 and Auritidibacter ignavus Yassin et al. 2011 based on features observed from Canadian and Swiss clinical isolates and wholegenome sequencing analysis
Fig. 1. Phylogenetic consensus tree based on nearly full-length 16S rRNA gene sequences. Phylogeny reconstructed with neighbourjoining (NJ), maximum-likelihood (ML) and maximum parsimony algorithms with NJ/ML/MP data respectively shown at nodes for type strains of type species of genera assigned to the family Micrococcaceae. The tree was calculated using MEGA X based on 1000 resamplings (bootstrap analysis, with only values ≥70% shown). Bar, 0.01 (NJ) or 0.02 (ML) substitutions per nucleotide position. The type strain of Cellulomonas flavigena was included as an unrelated outlier.
All Virus sequences originated for VIROPLANT by all partners and deposited in NCBI
<p>All Virus sequences originated for VIROPLANT by all partners and deposited in NCBI</p>
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T and other type strains of the genus Gordonia. Only values above 50% are shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, one nucleotide substitution per 100 nucleotides.
Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales
<p>The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (<i>Oncorhynchus nerka</i>), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous <i>O. nerka</i> in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan<span> </span>SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.</p>
Orca: Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale (Part1)
<p>This dataset (Part 1) provide the core resource files required for using the code of Orca, including models and the hg38 reference genome (resources_core.tar.gz), and the micro-C mcool files required for extracting the experimental observations (resources_mcools.tar.gz). Orca is a sequence-based deep learning modeling framework for multiscale genome 3D architecture.</p>
Single cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis
<p>Single <span>cell RNA sequencing (scRNAseq) is a powerful technique that continues to expand across various biological applications. However, incomplete 3' UTR annotations can impede single cell analysis resulting in genes that are partially or completely uncounted. Performing scRNAseq with incomplete 3' UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single cell isoform sequencing (ScISOr-Seq) in tandem with scRNAseq can rapidly improve 3' UTR annotations. Using threespine stickleback fish (</span><em>Gasterosteus aculeatus</em><span>), we show that gene models resulting from a minimal embryonic ScISOr-Seq dataset retained 26.1% greater scRNAseq reads than gene models from Ensembl alone. Furthermore, pooling our ScISOr-Seq isoforms with a previously published adult bulk Iso-Seq dataset from stickleback, and merging the annotation with the Ensembl gene models, resulted in a marginal improvement (+0.8%) over the ScISOr-Seq only dataset. In addition, isoforms identified by ScISOr-Seq included thousands of new splicing variants. The improved gene models obtained using ScISOr-Seq lead to successful identification of cell types and increased the reads identified of many genes in our scRNAseq stickleback dataset. Our work illuminates ScISOr-Seq as a cost-effective and efficient mechanism to rapidly annotate genomes for scRNAseq.</span></p>
Sequence diagram of the RIPOSTE framework
<p>Sequence diagram of the RIPOSTE framework</p>
Deep sequencing data for document titled: Rolling circle RNA synthesis catalysed by RNA
<p>RNA-catalysed RNA replication is widely considered a key step in the emergence of life's first genetic system. However, RNA replication can be impeded by the extraordinary stability of duplex RNA products, which must be dissociated for re-initiation of the next replication cycle. Here we have explored rolling circle synthesis (RCS) as a potential solution to this strand separation problem. RCS on small circular RNAs - as indicated by molecular dynamics simulations - induces a progressive build-up of conformational strain with destabilisation of nascent strand 5' and 3' ends. At the same time, we observe sustained RCS by a triplet polymerase ribozyme on small circular RNAs over multiple orbits with strand displacement yielding concatemeric RNA products. Furthermore, we show RCS of a circular Hammerhead ribozyme capable of self-cleavage and re-circularisation. Thus, all steps of a viroid-like RNA replication pathway can be catalysed by RNA alone. Our results have implications for the emergence of RNA replication and for understanding the potential of RNA to support complex genetic processes.</p>
Saluki: Predicting mRNA half-life from mRNA sequence
<p>Here we release datasets for Saluki, a hybrid deep convolutional and recurrent neural network, whose goal is to predict mRNA half-life from an mRNA sequence. Dataset can be analyzed with our associated Github code (https://github.com/vagarwal87/saluki_paper).</p>
FIGURE 3 in Two new species of Hypoxylon (Hypoxylaceae) from China based on morphological and DNA sequence data analyses
FIGURE 3. Hypoxylon jianfengense (Holotype FACATAS 845). A. Stromata on wood. B. Stromatal surface and ostioles. C, D. Stroma in vertical section showing the perithecia and tissue below the perithecial layer. E. KOH-extractable pigments. F. Stromatal granules in water. G. Mature and immature asci in water. H. Asci in Melzer's reagent. I. Immature asci in water. J, K. Mature asci in water. L. Apical apparatus in Melzer' s reagent. M. Ascospore in water showing germ slit. N. Ascospores in water. O. Ascospores in 10% KOH. P. Ascospore under SEM. Bars: A = 5 mm; B = 0.3 mm; C = 0.5 mm; D = 0.1 mm; G, I–K = 20 µm; H, L–O = 10 µm; P = 2.5 µm.
FIGURE 1 in Two new species of Hypoxylon (Hypoxylaceae) from China based on morphological and DNA sequence data analyses
FIGURE 1. Phylogenetic tree of Hypoxylon based on the multigene alignment of ITS-LSU-RPB2-TUB2 in the Maximum Likelihood analyses (RaxML). Support values of Maximum Likelihood (ML), Maximum Parsimony (MP) and Bayesian (B) analyses (bootstrap support above 50%, posterior probability value above 0.95) are displayed above or below the respective branches (ML/MP/BA).
FIGURE 2 in Two new species of Hypoxylon (Hypoxylaceae) from China based on morphological and DNA sequence data analyses
FIGURE 2. Hypoxylon larissae (Holotype FACATAS 844). A. Stromata on wood. B, C. Stromatal surface and ostioles. D, E. Stroma in vertical section showing the perithecia and tissue below the perithecial layer. F. KOH-extractable pigments. G. Stromatal granules in water. H. Mature and immature asci in Melzer's reagent. I. Asci in Melzer's reagent. J. Immature asci in water. K. Mature asci in water. L. Ascospores in water. M. Ascospores in 10% KOH. N. Ascospores in water showing germ slit. O. Apical apparatus in Melzer's reagent. P. Ascospore under SEM. Bars: A = 5 mm;B, C, E = 0.4 mm; D = 1 mm; H–K = 20 µm; L–O = 10 µm; P = 5 µm.
Raw data of sequencing results of our study: Bovine milk microbiota: Evaluation of different DNA extraction protocols in challenging samples
<p>Clean reads of the repeated milk samples with used Primer Pairs V1V2 and V3V4</p> <p>Raw data of sequencing results (amplicon single variants)</p>
Data for "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection"
<p>Once decompressed, the file contains a folder which contains:</p> <ul> <li>The files "s100_Nth.fasta" (where "N" is 5, 6, 7 or 8), which are the output of the SELEX experiment described in the paper with DOI: <a href="https://doi.org/10.1002/cbic.201900265">10.1002/cbic.201900265</a>. They are standard fasta files, and the descriptor of each sequence is of the form "seqX-Y", where "X" is an increasing label, and "Y" is the number of times "seqX" has been obtained (number of counts of "seqX").</li> <li>The file "Aptamer_Exp_Results.csv", which contains the sequences tested experimentally for the paper "Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection" (preprint available at https://doi.org/10.1101/2022.03.12.484094), with the following experimental results for each sequence: (i) whether the sequence was able to bind thrombin ('B' for binders, 'NB' for non-binders); (ii) the thrombin exosite used for binding ('I' for exosite I, 'II' for exosite II, 'n/a' for sequences not tested).</li> </ul> <p>Examples of usage of the data are available at https://github.com/adigioacchino/RBMsForAptamers.</p>
Figure 3. Bayesian maximum clade credibility tree constructed from whole mitochondrial genome sequences, with a in Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo
Figure 3. Bayesian maximum clade credibility tree constructed from whole mitochondrial genome sequences, with a focus on Bornean Crocidura. Reconstructed with BEAST2. Dates are indicated on nodes and bar on bottom. Nodes used to calibrate the dating are marked with a black square. Uropsilus and Soricinae outgroups were included in the phylogenetic analysis for calibration purposes but removed from the figure for clarity. Since most nodes are highly supported (PP> 0.95), only less supported nodes (0.95 0.80) are marked with an orange circle. Colours on the vertical bar indicate geographical origin of sampled animals, and colors match the map. Samples from north of Kra are shown in grey.
Magnetic bead epicPCR with dMLA probes, sequencing data, March 11 2022
<p>Samples:</p> <p>1. Mocks, 16S, 55°C<br> 2. HAMBIs+Mocks, 16S, 55°C<br> 3. HAMBIs, 16S, 55°C<br> 4. Mocks, 16S, 60°C<br> 5. HAMBIs+Mocks, 16S, 60°C<br> 6. HAMBIs, 16S, 60°C<br> 7. Mocks, 16S, 65°C<br> 8. HAMBIs+Mocks, 16S, 65°C<br> 9. HAMBIs, 16S, 65°C<br> 10. Mocks, dMLA, 55°C<br> 11. HAMBIs+Mocks, dMLA, 55°C<br> 12. HAMBIs, dMLA, 55°C<br> 13. Mocks, dMLA, 60°C<br> 14. HAMBIs+Mocks, dMLA, 60°C<br> 15. HAMBIs, dMLA, 60°C<br> 16. Mocks, dMLA, 65°C<br> 17. HAMBIs+Mocks, dMLA, 65°C<br> 18. HAMBIs, dMLA, 65°C<br> 19. Chilomonas, 16S<br> 20. Chilomonas+WW, 16S<br> 21. WW, 16S<br> 22. Chilomonas, 18S<br> 23. Chilomonas+WW, 18S<br> 24. WW, 18S</p>
FIGURE. Phylogenetic analysis of Chrysosporium spp. based on ITS sequences. Statistical support values (≥50 %) are shown at nodes, and presented as ML bootstrap support/Bayesian posterior probabilities. Names in black bold are the strains isolated in this study, the coloured names are the new species. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Phylogenetic analysis of Chrysosporium spp. based on ITS sequences. Statistical support values (≥50 %) are shown at nodes, and presented as ML bootstrap support/Bayesian posterior probabilities. Names in black bold are the strains isolated in this study, the coloured names are the new species.
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>Supplementary Table 2-1. Samples and assembly summary <br> Supplementary Table 2-2. CRISPR-targeted TR sequence summary</p>
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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.