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99 results for “Sanger”
MIR142 Sanger sequencing results in MPNs
<p>To extend and complement knowledge about the occurrence and/or frequency of <em>MIR142</em> mutations in hematologic cancers, we sequenced <em>MIR142</em> in large panels of MPNs [including polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF), and chronic myeloid leukemia (CML)], blood disorders for which such mutations have never been tested, and in AML and CLL, for which the mutations have been reported. The dataset gathers Sanger sequencing results of the <em>MIR142</em> locus.</p>
HLA class I Sanger sequences data of Honduras HIV cohort
<p>HLA polymorphisms represent the strongest genetic modifier of HIV disease progression. Diverse HLA distribution can lead to distinct HIV control landscapes at the population level. We aimed to describe HLA allele and haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency and the impact of these variants on HIV disease outcome. HLA class I (cI) loci were typed at 4-digit resolution, and CCR5 variants were determined in 402 HIV clade B-infected, ART-naïve individuals from Honduras. HLA LD were assessed using Fisher's exact test. Using univariable and multivariable analyses we evaluated HLA associations with HIV pVL and CD4 counts. We did not find any effect on HIV control between CCR5 genotypes. Previously defined HLA associations were found: <em>B*57:01/03</em>, <em>B*42:01</em>, <em>A*25:01</em> and <em>C*12:03</em> (protective), and <em>B*53:01</em> and <em>A*68:01</em> (risk). Being consistent with our previous research in a Mesoamerican HIV cohort, Amerindian <em>B*35:12</em> was associated to poor HIV control. Other HLA-HIV associations not previously described were <em>C*03:04</em> and <em>B*08:01</em> that were associated with higher pVL. Overall, this first report highlights the immunogenetic uniqueness admixture of the Honduras population that express Amerindian, Caucasian and African HLA subtypes. These findings not only support this cohort as ideal for identifying HLA correlates of HIV control but also may improve future research regarding allotransplantation and disease association.</p>
Data for a preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): exploring the combination of targeted enrichment data and legacy Sanger sequence data
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Phylogenetic data for construction of bryophyte tree using published sanger data
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Ultraconserved element data for phylogenomic analysis and four-gene Sanger dataset for phylogenetic analysis of Tenkana, a new genus of plexippine jumping spider (Salticidae, Plexippini, Plexippina)
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Sanger sequences of marpissoid salticids for Kelawakaju placement
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Rare and widespread: Integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma
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Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos
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HLA class I Sanger sequences data of Honduras HIV cohort
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Data from: Genomic footprint of cladogenesis revealed through RADseq and Sanger sequencing demonstrates congruent patterns in the velvet worm Peripatopsis sedgwicki species complex (Onychophora: Peripatopsidae)
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Data from: Information dropout patterns in restriction site associated DNA phylogenomics and a comparison with multilocus Sanger data in a species-rich moth genus
A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, RAD (Restriction site Associated DNA) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for non-model species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely un-investigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6,172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3,256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.
Data from: Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data
<p>Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially at the subfamily level, remain largely uncertain. Genomic data (83 taxa and 589 loci) were integrated with Sanger data (130 taxa and 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both data sets combined and analyzed separately, the monophyly of Gracillariidae and all its subfamilies, and the monophyly of the clade 'LAMPO' (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade 'AMO' (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (<i>Callicercops</i> Vári + Parornichinae) + Gracillariinae, as sister to the 'LAMPO' clade were supported by the best hypotheses. Based on these results, a new subfamily, Callicercopinae Li, Ohshima et Kawahara, is established to accommodate the enigmatic genus <i>Callicercops</i>. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the K-Pg extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves, and making galls, accelerated the diversification of Gracillariidae by avoiding larval parasitoids.</p>
Comprehensive survey of common bean viruses in Tanzania using next generation and Sanger sequencing techniques
<p>Common bean (<em>Phaseolus vulgaris</em> L.) is an important legume crop in Tanzania and elsewhere in the tropics and subtropics. We employed a next-generation sequencing technique to detect viruses in common bean plant samples collected from five agricultural research zones in the country. The aim was to target and sequence virus-derived small RNAs. To achieve this, total RNA was isolated from dry leaf samples using the CTAB method. The CTAB buffer contained 2% CTAB, 100 mM Tris–HCl, 20 mM EDTA, 2.5 M NaCl, freshly prepared 1% sodium sulfite, 2% PVP and 2.5% 2-mercaptoethanol in nuclease-free water. Total RNA was sent to Fasteris in Switzerland where the small RNA was purified by electrophoresis in an acrylamide gel. The small RNA library was prepared using the Illumina TrueSeq small RNA sample preparation kit (Illumina Inc., San Diego, CA, USA). Viruses were detected using VirusDetect software (v.1.6 and v.1.7) (available at http://bioinfo.bti.cornell.edu/cgi-bin/virusdetect/index.cgi) and supercomputer at CSC.fi. Viruses detected belonged to at least 11 genera.</p>
Sanger sequencing of target and off-target genomic regions for gene-edited iPSC clones with SETBP1 genetic variants
<p>This data set includes chromatograms generated using sanger sequencing of targeted regions of genomic DNA from clonal iPSC lines. The iPSC lines include clones generated using CRISPR/Cas9 homology directed repair to introduce genetic variants into <em>SETBP1,</em> and their wild-type controls. Additional files have been included in the data set to link chromatogram (ab1) files to specific iPSC clones for genomic regions across the variant in <em>SETBP1 (</em>SETBP1 clones genetic variant sanger sequencing.xslx)<em> </em>and top<em> </em>off-target sites (SETBP1 clones off-target sanger sequencing.xlsx). </p>
Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), using multilocus Sanger sequence and genomic ddRADseq data
<p>The Rough Greensnake, <i>Opheodrys aestivus,</i> is a moderately-sized, semi-arboreal snake broadly distributed throughout eastern North America. While numerous taxa with similar distributions have been shown to be comprised of multiple species, <i>O. aestivus</i> has yet to be examined in a detailed phylogeographic context. Here, we use Sanger-sequence data of one mitochondrial and three nuclear loci for samples from throughout the distribution of <i>O. aestivus</i> to elucidate phylogeographic patterns in this species. We combine this with ddRADseq data for a subset of samples to test patterns on a more genomically comprehensive scale. In both datasets, we find strong support for three deeply divergent clades within <i>O. aestivus</i>: peninsular Florida, central Texas, and a main clade comprising the rest of the distribution, with the Florida clade the earliest diverging lineage of the three. Estimates of divergence time suggest that the central Texas and main clades diverged approximately 1.34 million years ago (Mya), while the peninsular Florida clade diverged from other lineages approximately 2.94 Mya, and these lineages diverged from the sister taxon, <i>O. vernalis</i>, approximately 6.43 Mya.<i> </i>These results also suggest that the historically recognized Florida subspecies, <i>O. a. carinatus</i>, could be elevated to species status. While the divergence of peninsular Florida or central Texas populations is not unique among squamates, nor is low levels of divergence from the Atlantic coast to eastern Texas, this combination of patterns is unusual, and yields important insight into the biogeography of North American biota. Further, our approach helps illustrate how dense geographic sampling with limited genomic sequencing can be used as a guide for the selection of samples to test phylogeographic patterns comprehensively.</p>
Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
<p>The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family's major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we present a phylogeny inferred from nucleotide sequence data of 492 nuclear single-copy genes (230,915 aligned amino acid sites) from 94 species of Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae, Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target enrichment data. We find support for Amiseginae being more closely related to Cleptinae than to Chrysidinae. Furthermore, we find strong support for Allocoeliini being the sister lineage of all remaining Chrysidinae, while Elampini represent the sister lineage of Chrysidini and Parnopini. Our study corroborates results from a recent phylogenomic investigation which revealed Chrysidoidea as likely paraphyletic</p>
Supplemental data for: Classification of the Celastrales based on integration of genomic, morphological, and Sanger-sequence characters
<p>We present the best sampled phylogenetic analysis of Celastrales, with respect to both character and taxon sampling, and use it to present a natural classification of the order. Parnassiaceae are highly supported as sister to Celastraceae; we recognize both families as distinct. <em>Pottingeria</em> is highly supported as a member of an early derived lineage within Celastraceae. We recognize and circumscribe 13 subfamilies in Celastraceae, including the new subfamilies Crossopetaloideae, Maytenoideae, Microtropioideae, Monimopetaloideae, and Salaciopsioideae. We identified five genera that likely require generic recircumscriptions: <em>Cassine</em>, <em>Elachyptera</em>, <em>Gymnosporia</em>, <em>Salacia</em>, and <em>Semialarium</em>. Genera that had not been previously sampled in Sanger-sequence-based studies are resolved as follows: <em>Arnicratea</em> is sister to <em>Reissantia</em>, <em>Bequaertia</em> is in a clade with <em>Campylostemon</em> and <em>Tristemonanthus</em>, <em>Goniodiscus</em> is sister to <em>Wilczekra</em>, <em>Ptelidium</em> is nested within <em>Elaeodendron</em>, and <em>Tetrasiphon</em> is most closely related to <em>Gyminda</em>.</p>
Data for: Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Satyrinae, Nymphalidae)
<p>The diverse, largely Neotropical subtribe Euptychiina (Satyrinae, Nymphalidae) is widely regarded as one of the most taxonomically challenging groups among all butterflies. Over the last two decades, morphological and molecular studies have revealed widespread paraphyly and polyphyly among genera, and a comprehensive, robust phylogenetic hypothesis is needed to build a firm generic classification to support ongoing taxonomic revisions at the species level. Here, we generated a dataset which includes sequences for up to nine nuclear genes and the mitochondrial COI 'barcode' for a total of 1280 specimens representing 449 described and undescribed species of Euptychiina and 39 outgroups, resulting in the most complete phylogeny for the subtribe to date. In combination with a recently developed genomic backbone tree this dataset resulted in a topology with strong support for most branches. </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.
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.