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6,617 results for “RNA Sequencing”
Data from: Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family
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Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
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Single cell RNA sequencing of lateral and medial olivocochlear efferent neurons using PatchSeq
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RNA sequencing data from the guts of Drosophila wildtype and CG3740/nazo double mutant 20-day-old males
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RNA sequencing of nuclease dead PET127 conditions
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RNA sequencing results from SNA-high and SNA-low, young and old murine T cells
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RNA sequencing of PET127 mutants overexpressed using the galactose inducible promoter
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Spatial reconstruction of the early hepatic transcriptomic landscape after an acetaminophen overdose using single-cell RNA sequencing
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Deep sequencing data for document titled: Rolling circle RNA synthesis catalysed by RNA
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Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos
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RNA-sequencing endometrium intact, vasectomized, and control heifers
<p>An appropriate female reproductive environment is essential for pregnancy success. In several species, including mice, pigs and horses, seminal plasma (SP) components have been shown to modulate this environment, leading to increased embryo viability and implantation. Due to the characteristics of mating in the aforementioned species, SP comes into direct contact with the uterus. However, it is questionable whether any SP reaches the uterus in species that ejaculate inside the vagina, such as humans and cattle. Hence, we hypothesized that sperm, perhaps acting as a vehicle for SP factors, play a more important role in the modulation of the maternal uterine environment in these species. In addition, changes elicited by SP and/or sperm may originate in the vagina and propagate to more distal regions of the female reproductive tract. To test these hypotheses, a bovine model in which heifers were mated to intact or vasectomized bulls or were left unmated was used. RNA-sequencing of endometrial samples collected 24 h after mating with a vasectomized bull did not reveal any differentially expressed genes (DEGs) in comparison with control samples. However, the endometrium of heifers mated with intact bulls exhibited 24 DEGs when compared to heifers mated with vasectomized bulls, and 22 DEGs when compared to unmated control heifers. The expression of a set of cytokines (<em>IL6</em>, <em>IL1A</em>, <em>IL8</em>, and <em>TNFA</em>) and candidate genes identified in the endometrial RNA-sequencing (<em>PLA2G10</em>, <em>CX3CL1</em>, <em>C4BPA</em>, <em>PRSS2</em>, <em>BLA-DQB</em>, and <em>CEBPD</em>) were assessed by RT-qPCR in the vagina and oviductal ampulla. No differences in expression of these genes were observed between treatments in any region. However, mating to both intact and vasectomized bulls induced an increase in IL1A and TNFA expression in the vagina compared to the oviduct. These data indicate that sperm, but not secretions from the accessory glands alone, induce modest changes in endometrial gene expression after natural mating in cattle. However, it is not clear whether this effect is triggered by inherent sperm proteins or SP proteins bound to sperm surface at the time of ejaculation.</p>
Differential analysis of binarized single-cell RNA sequencing data captures biological variation
<p>Processed datasets used for binary differential analysis experiments.</p>
Data from: Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora
Ctenophores are a phylum of non-bilaterian marine (mostly planktonic) animals, characterised by several unique synapomorphies (e.g. comb rows, apical organ). Relationships between and within the nine recognised ctenophore orders are far from understood, notably due to a paucity of phylogenetically-informative anatomical characters. Previous attempts to address ctenophore phylogeny using molecular data (18S rRNA) led to poorly resolved trees but demonstrated the paraphyly of the order Cydippida. Here we compiled an updated 18S rRNA data set, notably including a few newly-sequenced species representing previously unsampled families (Lampeidae, Euryhamphaeidae), and we built up an additional more rapidly-evolving ITS1+5.8SrRNA+ITS2 alignment. These data sets have been analysed separately and in combination under a probabilistic framework, using different methods (Maximum Likelihood, Bayesian inference) and models (e.g. doublet model to accommodate secondary structure; data partitioning). An important lesson from our exploration of these datasets is that the fast-evolving ITS regions are useful markers for reconstructing high-level relationships within ctenophores. Our results confirm the paraphyly of the order Cydippida (and thus a "cyddipid-like" ctenophore common ancestor) and suggest that the family Mertensiidae could be the sister-group of all other ctenophores. The family Lampeidae (also part of the former "Cydippida") is probably the sister-group of the order Platyctenida (benthic ctenophores). The order Beroida might not be monophyletic, due to the position of Beroe abyssicola outside of a clade grouping the other Beroe species and members of the "Cydippida" family Haeckeliidae. Many relationships (i.e. between Pleurobrachiidae, Beroida, Cestida, Lobata, Thalassocalycida) remain unresolved. Future progress in understanding ctenophore phylogeny will come from the use of additional rapidly-evolving markers and improvement of taxonomic sampling.
Data from: Delimitation of the Thoracosphaeraceae (Dinophyceae), including the calcareous dinoflagellates, based on large amounts of ribosomal RNA sequence data
The phylogenetic relationships of the Dinophyceae (Alveolata) are not sufficiently resolved at present. The Thoracosphaeraceae (Peridiniales) are the only group of the Alveolata that include members with calcareous coccoid stages; this trait is considered apomorphic. Although the coccoid stage apparently is not calcareous, Bysmatrum has been assigned to the Thoracosphaeraceae based on thecal morphology. We tested the monophyly of the Thoracosphaeraceae using large sets of ribosomal RNA sequence data of the Alveolata including the Dinophyceae. Phylogenetic analyses were performed using Maximum Likelihood and Bayesian approaches. The Thoracosphaeraceae were monophyletic, but included also a number of non-calcareous dinophytes (such as Ensiculifera and Pfiesteria) and even parasites (such as Duboscquodinium and Tintinnophagus). Bysmatrum had an isolated and uncertain phylogenetic position outside the Thoracosphaeraceae. The phylogenetic relationships among calcareous dinophytes appear complex, and the assumption of the single origin of the potential to produce calcareous structures is challenged. The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future.
Data from: miR-122, small RNA annealing and sequence mutations alter the predicted structure of the Hepatitis C virus 5′ UTR RNA to stabilize and promote viral RNA accumulation
Annealing of the liver-specific microRNA, miR-122, to the Hepatitis C virus (HCV) 5′ UTR is required for efficient virus replication. By using siRNAs to pressure escape mutations, 30 replication-competent HCV genomes having nucleotide changes in the conserved 5′ untranslated region (UTR) were identified. In silico analysis predicted that miR-122 annealing induces canonical HCV genomic 5′ UTR RNA folding, and mutant 5′ UTR sequences that promoted miR-122-independent HCV replication favored the formation of the canonical RNA structure, even in the absence of miR-122. Additionally, some mutant viruses adapted to use the siRNA as a miR-122-mimic. We further demonstrate that small RNAs that anneal with perfect complementarity to the 5′ UTR stabilize and promote HCV genome accumulation. Thus, HCV genome stabilization and life-cycle promotion does not require the specific annealing pattern demonstrated for miR-122 nor 5′ end annealing or 3′ overhanging nucleotides. Replication promotion by perfect-match siRNAs was observed in Ago2 knockout cells revealing that other Ago isoforms can support HCV replication. At last, we present a model for miR-122 promotion of the HCV life cycle in which miRNA annealing to the 5′ UTR, in conjunction with any Ago isoform, modifies the 5′ UTR structure to stabilize the viral genome and promote HCV RNA accumulation.
A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing
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Healthy woodchuck genome with viral sequences appended used for single-cell RNA-seq analysis
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Curated RNA Sequencing Data for Zebrafish (Danio rerio) snoRNA Expression Analysis
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RNA sequencing of sorted conducting airway epithelial cells from FGF9-overexpressing and control mouse lungs at 1 day post-infection with IAV
<p><span>Influenza A virus (IAV) preferentially infects conducting airway and alveolar epithelial cells in the lung. The outcome of these infections is impacted by the host response, including the production of various cytokines, chemokines, and growth factors. Fibroblast growth factor-9 (FGF9) is required for lung development, can display antiviral activity <em>in vitro</em>, and is upregulated in asymptomatic patients during early IAV infection. We therefore hypothesized that FGF9 would protect the lungs from respiratory virus infection and evaluated IAV pathogenesis in mice that overexpress FGF9 in club cells in the conducting airway epithelium (FGF9-OE mice). However, we found that FGF9-OE mice were highly susceptible to IAV and Sendai virus infection compared to control mice. FGF9-OE mice displayed elevated and persistent viral loads, increased expression of cytokines and chemokines, and increased numbers of infiltrating immune cells as early as 1 day post-infection (dpi). Gene expression analysis showed an elevated type I interferon (IFN) signature in the conducting airway epithelium and analysis of IAV tropism uncovered a dramatic shift in infection from the conducting airway epithelium to the alveolar epithelium in FGF9-OE lungs. These results demonstrate that FGF9 signaling primes the conducting airway epithelium to rapidly induce a localized, protective IFN and proinflammatory cytokine response during viral infection. Although this response protects the airway epithelial cells from IAV infection, it allows for early and enhanced infection of the alveolar epithelium, ultimately leading to increased morbidity and mortality. Our study illuminates a novel role for FGF9 in regulating respiratory virus infection and pathogenesis.</span></p>
Probing the molecular basis of fruit firmness in southern highbush blueberry (Vaccinium corymbosum hybrid) through RNA sequencing
<p><span>Blueberries (<em>Vaccinium corymbosum L</em>.) benefit from increased fruit firmness because of consumer preference and machine harvestability. However, the genetic component of fruit texture and skin thickness and their relationship to firmness have yet to be deciphered. This study used bulked segregant RNA-seq (BSR-seq) for differential gene expression analysis. Previously an F1 population of a cross between firm-fruited southern highbush cv. 'Reveille' and soft-fruited cv. 'Arlen' was developed in our laboratory. The total RNA of the parents, the two softest, and the two firmest progenies, were extracted at the breaker and fully ripe stages. Next-generation sequencing cDNA libraries were constructed and subjected to Illumina short-read sequencing. Subsequently, the short reads were mapped to a blueberry genome, and differentially expressed genes (DEGs) were identified in immature and mature fruit coded for potentially biologically significant proteins such as expansins, polygalacturonase, polygalacturonase-inhibiting protein, and mannosidase. Additionally, DEGs corresponding to cysteine proteases and S-adenyl methyltransferases (SAM-MTases) that were previously reported as candidate genes for blueberry firmness were identified in this study. Our results indicated that BSR-seq is a promising method for identifying major candidate genes controlling complex traits in blueberry. </span></p>
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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.