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1,293 results for “gene sequencing”
Sequence alignment for 7 gene regions for new Phytophthora species in clade 2a
<p>Five new taxa from <i>Phytophthora</i> ITS Clade 2a are described from <i>Cinnamomum cassia</i> plantations and adjacent waterways in Van Yen, Vietnam, and disturbed rainforest in the Hela Province of Papua New Guinea and from disturbed forest on Christmas Island. Phylogenetic analyses were performed using data from nuclear regions (ITS, β-tubulin; Heat shock protein 90) and mitochondrial regions (cytochrome c oxidase subunit 1; cytochrome c oxidase subunit2; NADH dehydrogenase subunit 1; ribosomal protein L10). The molecular data supported recognition of three species: <i>Phytophthora insulinativitatica, P. multibullata </i>and <i>P. </i>x<i> vanyenensis</i> and two informal taxa, <i>P.</i> sp. germisporangia and <i>P.</i> sp. awatangi. <i>P. </i>x<i> vanyenensis</i> appears to be a hybrid between <i>P. </i>sp<i>. mekongensis</i> and an unknown species. <i>P. multibullata </i>and<i> P</i>. sp. germisporangia are phylogenetically close to <i>P. citrophthora,</i> but morphologically distinct. <i>P. insulinativitatica</i> is most closely related to <i>P. botryosa </i>but has different morphology.<b> </b><i>P.</i> sp. germisporangia and <i>P.</i> sp. awatangi were morphologically distinct and separated in the phylogeny based on mitochondrial sequences, but their nuclear sequences were identical. When comparing the sequences of these new species to that available on GenBank, it became evident that some of these species shared similarity with isolates submitted to GenBank under other species names and a re-evaluation of all P<i>. meadii</i> and <i>P. colocasiae</i> ITS sequence data identified an additional 7 putatively new species all isolated from Asia. The results support the view that many more <i>Phytophthora</i> species remain to be discovered in the Asia-Pacific region.</p>
Sequences of the 4 QRDR genes in the 39 NTS clinical isolates
<p>Sequences of the 4 QRDR genes (gyrA, gyrB, parC, and parE) in the 39 NTS clinical isolates</p>
Automated application to assist in detecting novel gene-disease associations following whole genome sequencing
<p>Results files, analysis scripts and original software from TierUp reanalysis performed on June 2020. These data contribute to the publication titled "Automated reanalysis application to assist in detecting novel gene-disease associations following whole genome sequencing". </p> <ul> <li> <p>tierup_v0-3-0.tar.gz - source code used in the reanalysis</p> </li> <li> <p>tierup_results_summary.tar.gz - raw data and python code for publication figures</p> </li> </ul> <p> </p>
Long-read genome sequencing accelerated the cloning of Pm69 by resolving the complexity of a rapidly evolving resistance gene cluster in wheat
<p>Oxford Nanopore assembly of <em>Triticum turgidum</em> ssp. <em>dicoccoides, </em>cv. G305-3M.</p>
Single-cell RNA sequencing of Sox17-expressing lineages reveals distinct gene regulatory networks and dynamic developmental trajectories
<p>Two seurat objects contains single-cell RNA sequencing data that captures <em>Sox17</em>-expressing lineages during embryogenesis.</p> <p>sox17_integrated_Figure2B.rds :</p> <p>This is a seurat object that contains single-cell RNA sequencing data from integration of GFP+ cells produced from <em>Sox17<sup>GFPCre</sup></em> allele marking cells that currently express <em>Sox17</em> or short-term progeny of <em>Sox17­-</em>expressing progenitors and TdTomato+ cells produced from <em>R26<sup>LSL.TdTomato</sup></em> reporter allele in the presence of <em>Sox17<sup>GFPCre</sup></em> marking long-term progeny of <em>Sox17</em>-expressing progenitors. Inferred cell types in this seurat object reflects Figure 2B in the article.</p> <p>sox17_Prox1_endoderm_Figure5A.rds :</p> <p>This is a seurat object that contain single-cell RNA sequencing data from integration of <em>Sox17</em>- and <em>Prox1</em>-expressing endoderm dataset. Prox-1 expressing endoderm data is from the Willnow et al. <em>Nature</em>(2021). Inferred cell types in this seurat object reflects Figure 5A in the article.</p>
Gene sequences for 2031 Saccharomyces cerevisiae genome assemblies
<p>Gene sequences for 2031 Saccharomyces cerevisiae genome assemblies</p>
Figure 6 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 6. Hypothetical radiation schemes for Uromastyx and possibly relevant geological events. Approximate distribution range for each taxon (Wilms, 2001) is shown with its abbreviated name: Hard (Uromastyx hardwickii), Aca (U. acanthinura), Mali (U. d. maliensis), Gey (U. geyri), Dis (U. d. dispar), Oce (U. ocellata), Mac (U. macfadyeni), Aeg (U. a. aegyptia), Mic (U. a. microlepis), Orn (U. ornata) and Ben (U. benti).
Figure 5 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 5. Neighbour-joining tree constructed based on maximum likelihood distances from 1503 alignable nucleotide sites (the HKY model and transition/transversion ratio of 3.48). The tree was rooted with Chamaeleo africanus as an outgroup. Bootstrap probabilities are shown for neighbour joining, maximum likelihood and maximum parsimony analyses (from left to right). Underlined values mean that the branch was not reconstructed in the best tree topology by the corresponding analyses. Note that two distinct sequence haplotypes are included for Uromastyx acanthinura and U. ocellata. See Material and methods for more details on the analytical conditions. The nucleotide sequences taken from the database are: Chamaeleo africanus (accession No., AF448743), Chlamydosaurus kingii (AF128469), Physignathus lesueurii (AF128463), Acanthosoura capra (AF128498), Salea horsfieldii (AF128490), Trapelus savignii (AF128512), Leiolepis guentherpetersi (AF128461), Leiolepis belliana (U82689), Laudakia caucasia (AF028681) and Laudakia lehmanni (AF028677).
Figure 4 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 4. Secondary structures of the inserted sequences found between tRNAGln and tRNAIle genes. The 128 bp insert for Uromastyx ornata can assume alternative secondary structures either with an extremely stable and long stem region (A) or with a clover-leaf structure for the second tRNAGln gene (or pseudogene) and a stable stem-and-loop structure (B). The 59 bp inserted for U. ocellata may also assume a somewhat less stable stem-and-loop structure (C). Heavy-strand sequences are shown and numbers refer to the corresponding positions in their light-strand sequences shown in Fig. 3A. Bars in stems represent Watson–Crick base pairs and dots stand for wobble G–U pairs for RNA.
Figure 2 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 2. Evolution of mitochondrial gene organization in Uromastyx. A, typical vertebrate organization plesiomorphic to lizards. B, typical organization for acrodont lizards including Leiolepis and likely the direct common ancestor of Leiolepis and Uromastyx. C, typical Uromastyx organization in which the putative origin of light-strand replication (black box) disappeared from the WANCY tRNA gene cluster. D, organization for U. ornata and likely for the direct common ancestor of U. ornata and U. ocellata, which has an insertion containing a stem-and-loop structure (hatched box) and the second tRNAGln gene or pseudogene (Q*). E, organization for U. ocellata in which Q* disappeared. See Figs 3 and 4 for sequences and secondary structures of the inserted region in U. ornata and U. ocellata.
Figure 3 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 3. Nucleotide sequences of the inserted region between the tRNA Gln and tRNAIle genes. A, alignment between the 128 bp insertion in Uromastyx ornata and the 59 bp insertion in U. ocellata (65% identity). B, alignment between the original tRNAGln gene and its second copy within the inserted region for U. ornata (49% identity). Light-strand and heavystrand sequences are shown for A and B, respectively. Dots indicate identity with the first sequence and dashes denote a gap.
Figure 1 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 1. Position of primers used for amplification and/or sequencing. See Table 1 for the primer sequences; numbers of primers correspond to those in Table 1.
Fig. 4. Amino acid sequences alignment between TCS1 and candidate N in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain
Fig. 4. Amino acid sequences alignment between TCS1 and candidate N-methyltransferase genes (GCS1, GCS2, and GCS3).
FIGURE 4 in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
FIGURE 4. Maximum Likelihood (ML) phylogeny inferred with dataset 3 that contains cox1 and ITS1 sequences concatenated. Tree scale corresponds to the number of substitutions per site. Numbers at nodes reflect the UFB support values proportional to size (showing only values from 70% to 100%). Countries of origin labelled as 3-digit alpha code: ESP (Spain), GBR (UK), NZL (New Zealand), PAN (Panama). Results from species in this study are highlighted in red (Australopacifica atrata), blue (Artioposthia exulans), and green (Marionfyfea adventor).
FIGURE 2. Maximum likelihood phylogeny inferred from cox1 in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
FIGURE 2. Maximum likelihood phylogeny inferred from cox1 sequences (dataset 1). Tree scale corresponds to the number of substitutions per site. Numbers at nodes correspond to the ultrafast bootstrap support values (showing only values from 70% to 100%). Countries of origin labelled as 3-digit alpha code: AUS (Australia), BRA (Brazil), ESP (Spain), FRA (France), GBR (UK), NZL (New Zealand), PAN (Panama). Results from species in this study are highlighted in red (Australopacifica atrata), blue (Artioposthia exulans), and green (Marionfyfea adventor).
FIGURE 3 in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
FIGURE 3. ML phylogeny inferred from ITS1 sequences (dataset 2). Tree scale corresponds to the number of substitutions per site. Numbers at nodes reflect the UFB support values (showing only values from 70% to 100%). Countries of origin labelled as 3-digit alpha code: ESP (Spain), GBR (UK), NZL (New Zealand), PAN (Panama). Results from species in this study are highlighted in red (Australopacifica atrata) and blue (Artioposthia exulans).
FIGURE 1. a in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
FIGURE 1. a, Marionfyfea adventor, the sequenced UK specimen, anterior to the left, length ca 1cm. GenBank Acc. Number OQ789899 (photo HDJ); b, Marionfyfea adventor, the sequenced Brittany specimen, anterior to the right, length ca 1cm. GenBank Acc. Number OQ789900 (photo EM); c, longitudinal section of the copulatory apparatus of the Brittany specimen, anterior to the right (ad = adenodactyls, p = penis). GenBank Acc. Number OQ789900 (photo MÁ-P); d, Artioposthia exulans, a specimen from Ireland collected by Julia Cooper, anterior to the left, damaged posterior, length ca 1.2cm (photo HDJ); e, Australopacifica atrata, specimens collected from Sally Barratt's garden in Manchester, feeding on chicken liver in captivity (photo HDJ); f, Microplana cf. edwardsi, the sequenced specimen from Gloucestershire, anterior to the left, length <1cm. GenBank Acc. Number OQ789902 (photo EM); g, Microplana cf. edwardsi, a sequenced specimen from Cumbria, anterior to the left, length <1cm. GenBank OQ789903 Acc. Number (photo EM); h, Microplana cf. edwardsi, a sequenced specimen from Cumbria, anterior to the left, length <1cm. GenBank Acc. Number OQ789904 (photo EM).
FIGURE 5 in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
FIGURE 5. ML phylogeny inferred with dataset 4 including species from the Microplana genus and using Bipaliinae as outgroup. Tree scale corresponds to the number of substitutions per site. Numbers at nodes reflect the UFB support values being proportional to size (showing only values from 70% to 100%). Results from Microplana cf. edwardsi are highlighted in red. Countries of origin labelled as 3-digit alpha code: BGR (Bulgaria), ESP (Spain), FRA (France), GBR (UK), ITA (Italy) PRT (Portugal). The photographs are of specimens with a small-white morphotype of the numbered species (photos EM).
Supplementary Figure 2 in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
Supplementary Figure 2. BI phylogeny inferred with ITS1 sequences in dataset 2. Numbers at nodes reflect the PP values (showing only values from 0.85 to 1.00). Tree scale corresponds to the number of substitutions per site.
Supplementary Figure 3 in Exploring gene sequences and phylogenetic relationships of four terrestrial planarian species (Platyhelminthes; Tricladida; Geoplanidae) in Europe
Supplementary Figure 3. BI phylogeny inferred with the concatenated dataset (dataset 3). Numbers at nodes reflect the PP values (showing only values from 0.85 to 1.00). Tree scale corresponds to the number of substitutions per site.
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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.