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2,556 results for “RNAseq”
Generating VISA scores on glioma bulk RNAseq and single cell RNAseq glioma
<p>Tissue stiffness is collectively determined by the stiffness of ECM and cells. Gliomas are characterized by dysregulated expression of ECM proteins, ECM crosslinking enzymes, and aberrant cellular contractility.While The RNA sequencing datasets have been comprehensively analyzed to interrogate tumor genomes, epigenomes, and transcriptomes, we realized an untapped potential: using transcriptomic data coupled with analysis of gene expression associated with ECM and actomyosin contractility to establish a bioinformatic tool, which we named VIrtual Stiffness Algorithm (VISA), capable of inferring tissue stiffness.</p> <p>This data repository is for reproducing VISA scores on glioma bulk RNAseq and single cell RNAseq glioma.</p>
Bulk RNAseq of K7M2 osteosarcoma cells in engineered bone marrow treated with Doxorubicin
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DNA-PKcs RNASeq data: DNA-PKcs wilde-type or kinase-dead protein regulate basal and etoposide-induced gene expression changes
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RNAseq, virulence, and phylogenetics studies of the gene easR of Metarhizium brunneum
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Male and female adult zebra finch (Taeniopygia guttata) gonad RNAseq associated with: Relaxed purifying selection maintains a sex-linked supergene polymorphism in zebra finches
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RNAseq transcriptome of draining lymph node (LN) and tumor of MC38 murine tumors treated with cryoablation and chitosan/IL-12
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RNAseq data of iRECs treated with palmitic acid and oleic acid
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Loricarioid catfish evolved skin denticles that recapitulate teeth at the structural, developmental, and genetic levels (raw RNAseq reads)
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RNAseq data relating to manuscript: Prior Fc Receptor activation primes macrophages for increased sensitivity to IgG via long term and short term mechanisms.
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RNAseq analysis of heart samples collected from wild-type and ZNF768 null mice 8 hours post-irradiation
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Adaptation to starvation requires a flexible circadian clockwork in Neurospora crassa (RNAseq)
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Bulk RNAseq of chronic LPS treated female mouse pituitary across doses
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RAW data: Knockdown of UTX/KDM6A Enriches Precursor Cell Populations in Urothelial Cell Cultures and Cell Lines - single cell RNAseq - Fastq format and UMI counts
<p>This data set of the single cell sequencing experiment of the urothelial cell line HBLAK belongs to the publication: "Knockdown of UTX/KDM6A Enriches Precursor Cell Populations in Urothelial Cell Cultures and Cell Lines" Cancers 2020, 12(4), 1023; https://doi.org/10.3390/cancers12041023.</p> <p> </p>
Irisin directly stimulates osteoclastogenesis and bone resorption in vitro and in vivo: RNAseq dataset
Irisin, a skeletal-muscle secreted myokine, facilitates muscle-bone crosstalk and skeletal remodeling in part by its action on osteoblasts and osteocytes. In this study, we investigated whether irisin directly regulates osteoclasts. In vitro, irisin (2–10 ng/mL) increased osteoclast differentiation in C57BL/6J mouse bone marrow progenitors; however, this increase was blocked by a neutralizing antibody to integrin αVβ5. Irisin also increased bone resorption on several substrates in situ. RNAseq revealed differential gene expression induced by irisin including upregulation of markers for osteoclast differentiation and resorption, as well as osteoblast-stimulating 'clastokines'. Forced expression of the irisin precursor Fndc5 in transgenic C57BL/6J mice resulted in lower bone mass at three ages and greater in vitro osteoclastogenesis from Fndc5-transgenic bone marrow progenitors. This study demonstrates that irisin acts directly on osteoclast progenitors to increase differentiation and promote bone resorption, supporting the tenet that irisin not only stimulates bone remodeling but may also be an important counter-regulatory hormone.
Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus
<p><span><i>Wolbachia</i> is a maternally transmitted bacterium that manipulates arthropod and nematode biology in myriad ways. The <i>Wolbachia</i> strain colonizing <i>Drosophila melanogaster</i> creates sperm-egg incompatibilities and protects its host against RNA viruses, making it a promising tool for vector control. Despite successful trials using <i>Wolbachia</i>-transfected mosquitoes for Dengue control, knowledge of how <i>Wolbachia</i> and viruses jointly affect insect biology remains limited. Using the <i>Drosophila melanogaster </i>model, transcriptomics and gene expression network analyses revealed pathways with altered expression and splicing due to <i>Wolbachia</i> colonization and virus infection. Included are metabolic pathways previously unknown to be important for <i>Wolbachia</i>-host interactions. Additionally, <i>Wolbachia</i>-colonized flies exhibit a dampened transcriptomic response to virus infection, consistent with early blocking of virus replication. Finally, using <i>Drosophila</i> genetics, we show <i>Wolbachia</i> and expression of nucleotide metabolism genes have interactive effects on virus replication. Understanding the mechanisms of pathogen blocking will contribute to the effective development of <i>Wolbachia</i>-mediated vector control programs.</span></p>
Proteinuric chronic kidney disease mouse model RNAseq
<p>RNA seq in renal cortex from proteinuric CKD mouse model</p>
RNAseq raw counts FLCN positive vs. FLCN negative renal proximal tubular epithelial cells (RPTEC)
<p>Germline inactivating mutations in Folliculin (FLCN) cause Birt–Hogg–Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing to kidney tumors. FLCN is a conserved, essential gene linked to diverse cellular processes but the mechanisms by which FLCN prevents kidney cancer remain unknown. Here we show that deleting FLCN activates TFE3, upregulating its downstream E-box genes in human renal tubular epithelial cells (RPTEC/TERT1), including RRAGD and GPNMB, without modifying mTORC1 activity. Surprisingly, deletion of FLCN or its binding partners FNIP1/FNIP2 also induces interferon response genes, but independently of interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to chromatin and slows cellular proliferation. Our integrated analysis identifies STAT1/2 signaling as a novel target of FLCN in renal cells and BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed hyper-proliferation and may influence the immune response. These findings shed light on unique roles of FLCN in human renal tumorigenesis and pinpoint candidate prognostic biomarkers.</p>
RNAseq data for Red-Face Hereford Carcass Quality Pooled Samples
<p>Fold change and FPKM data from RNAseq of Muscle tissue samples from Red-Faced Herefords of differing carcass quality collected at harvest.</p>
Data from: The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq
Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of a wild species of sunflowers (Helianthus spp.) and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs) in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha) and identified gene ontology categories with elevated values of alpha. The "response to biotic stimulus" category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio) and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity [pi]). We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence.
RNASeq - Web App Dataset
<p>This is a dataset containing RNASeq data used in an RShiny web app. This app is connected to a publication and is used as a visualisation tool.</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.