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1,353 results for “single-cell transcriptomics”
Immune Signature of Chronic Hand Eczema Unveiled by Spatial Transcriptomics and Single-Cell Proteomics
ClinicalTrials.gov study NCT06884163. IPD Sharing: NO. Countries: 1. Publications: 6.
Molecular Taxonomy of Surgically-harvested Ocular Tissues Defined by Single-cell Transcriptomics
ClinicalTrials.gov study NCT04682054. IPD Sharing: YES. Countries: 1. Publications: 4.
Data from: Division of functional roles for termite gut protists revealed by single-cell transcriptomes
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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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Integrative analyses of single-cell transcriptome and immune profiling reveal clonal expansion of T cells in the blood and cerebrospinal fluid of Parkinson's disease
<p>An increasing number of studies has indicated that the immune system plays important roles in the pathogenesis of Parkinson's disease. However, little is known about the contribution of adaptive immune responses in Parkinson's disease. Here, we performed comprehensive integrative analyses of single-cell transcriptome and immune profiling of the blood of 8 Parkinson's patients and 13 healthy controls as well as the cerebrospinal fluid of 6 Parkinson's patients, 4 Alzheimer's patients, 5 mild cognitive impairment (MCI) patients and 9 healthy controls. In total, 22 T cell subsets with distinct functions and clonalities were identified from 121,402 T cells. We observed significant clonal expansion of effector CD8+ T cells in Parkinson's patients, which formed a gradient of transcriptional states from central memory CD8+ T cells to early effector CD8+ T cells followed by terminal effector CD8+ T cells. Shared TCRs in this progression suggest TCRs may be involved in the state transition of CD8+ T cells stimulated by antigens. Notably, we also found that a group of clonally expanded cytotoxic CD4+ T cells were significantly increased in Parkinson's patients compared to controls, suggesting their cytotoxic roles in Parkinson's disease. Finally, we screened putative TCR-antigen pairs that existed in both blood and cerebrospinal fluid of patients with Parkinson's disease. These results reveal an adaptive immune response in the blood and cerebrospinal fluid of Parkinson's disease and provide novel evidence of clonal, antigen-experienced T cells patrolling in the blood and cerebrospinal fluid of Parkinson's disease.</p>
Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs
<p>Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid <em>Olkasia</em> as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by <em>Ploeotia</em> spp.), <em>Lentomonas</em>, and <em>Keelungia</em> form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes <em>Rapaza</em>, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (<em>Anisonema</em> and <em>Dinema</em> spp.), '<em>Heteronema</em> II' (represented by <em>H. vittatum</em>), and a clade of <em>Neometanema</em> plus Aphagea. Among 'peranemid' phagotrophs, <em>Chasmostoma</em> branches with included <em>Urceolus</em>, and <em>Peranema</em> with the undescribed '<em>Jenningsia</em> II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that <em>Entosiphon</em> is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.</p>
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data
<p>This dataset contains gene expression values, i. e. transcript counts, of 278 intestinal epithelial cells.</p>
Cellular and molecular heterogeneities and signatures, and pathological trajectories of fatal COVID-19 lungs defined by spatial single-cell transcriptome analysis
<p>Spatial in-situ data analysis.</p>
Single-Cell and Spatial Transcriptomics Analysis of Steatotic Donor Liver Susceptibility to Post-Transplant Injury
ClinicalTrials.gov study NCT07362745. IPD Sharing: NO. Countries: 1. Publications: 0.
Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs
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Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics [10X_scRNAseq]
GEO Series GSE141589. Drosophila melanogaster. 1 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptomes and T cell receptor sequences of memory T lymphocytes from the peripheral blood and the synovial fluid of patients with juvenile idiopathic arthritis.
GEO Series GSE160097. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing.
Single-cell and single-nucleus transcriptome analysis of pattern formation in the early embryo of the spider Parasteatoda tepidariorum
GEO Series GSE201705. Parasteatoda tepidariorum. 3 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
GEO Series GSE202210. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Spatial Transcriptomics and Single-Cell RNA-Sequencing Revealed Dendritic Cell-Mediated Inflammation in Keratoconus
GEO Series GSE285060. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multi-compartmental alterations in gene expression and signaling cross-talk
GEO Series GSE274068. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
GEO Series GSE81861. Homo sapiens. 1220 samples. Type: Expression profiling by high throughput sequencing.
The dynamics of cellular response to therapeutic perturbation using multiplexed quantification of the proteome and transcriptome at single-cell resolution
GEO Series GSE100501. Homo sapiens. 31 samples. Type: Expression profiling by high throughput sequencing; Other.
Single-cell transcriptomic analyses of pancreatic islets reveals islet cell-type-specific adaptations to pregnancy and the postpartum
GEO Series GSE226788. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptome profiling of the stepwise progression of head and neck cancer
GEO Series GSE181919. Homo sapiens. 37 samples. Type: Expression profiling by high throughput sequencing.
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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.