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55 results for “spatial signature”
Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population
<p>This record contains all the fully processed single cell RNA sequencing objects included in the paper Nyirenda et al (2024) '<em>Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population</em>'. </p> <h3>Abstract</h3> <p><em>Postmortem single-cell studies have transformed understanding of lower respiratory tract diseases (LRTD) including Covid19, but there is minimal data from African settings where HIV, malaria and other environmental exposures may affect disease pathobiology and treatment targets. We used histology and high-dimensional imaging to characterise fatal lung disease in Malawian adults with (n=9) and without (n=7) Covid19, and generated single-cell transcriptomics data from lung, blood and nasal cells. Data integration with other cohorts showed a conserved Covid19 histopathological signature, driven by contrasting immune and inflammatory mechanisms: in USA, European and Asian cohorts by type I/III interferon responses, particularly in blood-derived monocytes, in the Malawi cohort, by response to interferon-gamma (IFN-γ) in lung-resident macrophages. HIV status had minimal impact on histology or immunopathology. Our study provides a data resource and highlights the importance of studying the cellular mechanisms of disease in underrepresented populations, indicating shared and distinct targets for treatment. </em></p> <h3>Figure 3</h3> <p>COSMIC_Lung_Atlas.h5ad</p> <p>COSMIC_Lung_Stromal_Atlas.h5ad</p> <p>COSMIC_Lung_Immune_Atlas.h5ad</p> <h3>Figure 4</h3> <p>COSMIC_HCLA_Integration.rds</p> <h3>Figure 5</h3> <p>COSMIC_Nasal_Atlas.h5ad</p> <p>COSMIC_Blood_Atlas.h5ad</p> <h3>Total Post-mortem COVID-19 Lung Autopsy Papers Integration</h3> <p>This data object was generated whereby all publicly available fatal COVID-19 lung single cell cohorts were integrated together. We include this analysis to show that the observed interferon responses detailed in the paper are preserved in not only the HLCA, but also existing post-mortem lung cohorts. The codebase for this additional analysis can be found here: <strong><a href="https://github.com/olympiahardy/Malawi_Integration">https://github.com/olympiahardy/Malawi_Integration</a> </strong></p> <p>COSMIC_Delorey_Melms_Integration.rds</p> <p> </p> <p> </p> <h3>Imaging Mass Cytometry Analysis</h3> <p>This Zenodo record can be accessed using the DOI here: <strong><a href="10.5281/zenodo.13899297">10.5281/zenodo.13899297</a> </strong>. The GitHub repository can be accessed here:<strong> <a href="https://github.com/joaolsf/Spatial_Single_Cell_Lung_Atlas_Malawi_COVID">https://github.com/joaolsf/Spatial_Single_Cell_Lung_Atlas_Malawi_COVID</a></strong></p> <p> </p>
Single-cell and spatial RNA sequencing identify divergent microenvironments and progression signatures in early- versus late-onset prostate cancer
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Data from: Signatures of human impact: size distributions and spatial organization of wetlands in the prairie pothole landscape
More than 50% of global wetland area has been lost over the last 200 years, resulting in losses of habitat and species diversity as well as decreased hydrologic and biogeochemical functionality. Recognition of the magnitude of wetland loss as well as the wide variety of ecosystem services provided by wetlands has in recent decades led to an increased focus on wetland restoration. Restoration activities, however, often proceed in an ad-hoc manner, with a focus on maximizing the total restored area rather than on other spatial attributes of the wetland network, which are less well understood. In this study, we have addressed the question of how human activities have altered the size distribution and spatial organization of wetlands over the Prairie Pothole Region of the Des Moines Lobe using high-resolution LIDAR data. Our results show that as well as the generally accepted 90% loss of depressional wetland area, there has been a disproportionate loss of both smaller and larger wetlands, with a marked alteration of the historical power-law relationship observed between wetland size and frequency and a resulting homogenization of the wetland size distribution. In addition, our results show significant decreases in perimeter-to-area ratios, increased mean distances between wetlands, particularly between smaller wetlands, and a reduced likelihood that current wetlands will be located in upland areas. Such patterns of loss can lead to disproportionate losses of ecosystem services, as smaller wetlands with larger perimeter-to-area ratios have been found to provide higher rates of biogeochemical processing and groundwater recharge, while increased mean distances between wetlands hinder species migration and thus negatively impact biodiversity. These results suggest the need to gear restoration efforts towards understanding and recreating the size distribution and spatial organization of historical wetlands, rather than focusing primarily on an increase in overall area.
Molecular and spatial signatures of human and rat corpus cavernosum physio-pathological processes at single-cell resolution
<p><span>The composition and cellular heterogeneity of the corpus cavernosum (CC) microenvironment has been characterized, but the spatial heterogeneity at the molecular level remains unexplored. In this study, we integrate single-cell RNA sequencing (scRNA-seq) and spatial transcriptome sequencing to comprehensively chart the spatial cellular landscape of human and rat CC under normal and disease conditions. We observe differences in the proportion of cell subtypes and marker genes between humans and rats. Based on the analysis of the fibroblasts (FB) niche, we also find that the enrichment scores of mechanical force signaling vary across different regions and correlate with the spatial distribution of FB subtypes. In vitro, the soft and hard extracellular matrix (ECM) induces the differentiation of FB into APO+FB and COMP+FB, respectively. In summary, our study provides a cross-species and </span><span>physio-pathological</span><span> </span><span>transcriptomic atlas of the CC, contributing to a further understanding of the molecular anatomy and regulation of penile erection.</span></p>
Spatially resolved single-cell atlas unveils A distinct cellular signature of fatal lung COVID-19 in a Malawian population
<p>Postmortem single-cell studies have transformed understanding of lower respiratory tract diseases (LRTD) including Covid19, but there is minimal data from African settings where HIV, malaria and other environmental exposures may affect disease pathobiology and treatment targets. We used histology and high-dimensional imaging to characterise fatal lung disease in Malawian adults with (n=9) and without (n=7) Covid19, and generated single-cell transcriptomics data from lung, blood and nasal cells. Data integration with other cohorts showed a conserved Covid19 histopathological signature, driven by contrasting immune and inflammatory mechanisms: in USA, European and Asian cohorts by type I/III interferon responses, particularly in blood-derived monocytes, in the Malawi cohort, by response to interferon-gamma (IFN-γ) in lung-resident macrophages. HIV status had minimal impact on histology or immunopathology. Our study provides a data resource and highlights the importance of studying the cellular mechanisms of disease in underrepresented populations, indicating shared and distinct targets for treatment. </p> <p>Here, there are scripts containing pre-processing, image denoise, cell segmentation, single-cell and spatial statistics analysis as well as visualisation plots for the Imaging Mass Cytometry of the post-mortem lung sections. </p> <p>Check out the interactive single cell atlas hosted on the cellxgeneVIP platform hosted by the University of Glasgow, by clicking on <a href="https://cellatlas-cxg.mvls.gla.ac.uk/COSMIC/view/COSMIC_IMC_Lung.h5ad/" rel="nofollow">https://cellatlas-cxg.mvls.gla.ac.uk/COSMIC/view/COSMIC_IMC_Lung.h5ad/</a></p>
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.
Spatially Transcriptomics Reveals Molecular Signatures in CRPS
ClinicalTrials.gov study NCT05986461. IPD Sharing: NO. Countries: 1. Publications: 7.
Data from: Signatures of human impact: size distributions and spatial organization of wetlands in the prairie pothole landscape
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Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes
The spatial structure of the environment (e.g., the configuration of habitat patches) may play an important role in determining the strength of local adaptation. However, previous studies of habitat heterogeneity and local adaptation have largely been limited to simple landscapes, which poorly represent the multi-scale habitat structure common in nature. Here, we use simulations to pursue two goals: (1) we explore how landscape heterogeneity, dispersal ability, and selection affect the strength of local adaptation, and (2) we evaluate the performance of several genotype-environment association (GEA) methods for detecting loci involved in local adaptation. We found that the strength of local adaptation increased in spatially aggregated selection regimes, but remained strong in patchy landscapes when selection was moderate to strong. Weak selection resulted in weak local adaptation that was relatively unaffected by landscape heterogeneity. In general, the power of detection methods closely reflected levels of local adaptation. False positive rates (FPRs), however, showed distinct differences across GEA methods based on levels of population structure. The univariate GEA approach had high FPRs (up to 55%) under limited dispersal scenarios, due to strong isolation by distance. By contrast, multivariate, ordination-based methods had uniformly low FPRs (0-2%), suggesting these approaches can effectively control for population structure. Specifically, constrained ordinations had the best balance of high detection and low FPRs, and will be a useful addition to the GEA toolkit. Our results provide both theoretical and practical insights into the conditions that shape local adaptation and how these conditions impact our ability to detect selection.
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>
Data from: Genomic signatures of spatially divergent selection at clownfish range margins
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Data from: Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes
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Extraction of a Stromal Metastatic Gene Signature in Breast Cancer via Spatial Profiling
GEO Series GSE273439. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Spatial multi-omics defines a shared glioblastoma infiltrative signature at the resection margin [10x Spatial]
GEO Series GSE286413. Homo sapiens. 2 samples. Type: Other.
Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived β-Like Cells
GEO Series GSE188827. Homo sapiens. 28 samples. Type: Expression profiling by high throughput sequencing.
Spatial transcriptomics from paired pancreas and associated draining lymph nodes reveals a lymphotoxin-beta signature in human type 1 diabetes
GEO Series GSE296626. Homo sapiens. 36 samples. Type: Other.
Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex
GEO Series GSE226211. Mus musculus. 17 samples. Type: Expression profiling by high throughput sequencing; Other.
Spatial Transcriptomics of Meningeal Inflammation Reveals Variable Penetrance of Inflammatory Gene Signatures into Adjacent Brain Parenchyma
GEO Series GSE236963. Mus musculus. 11 samples. Type: Expression profiling by high throughput sequencing.
Spatially Resolved Transcriptomic Signatures of Hippocampal Subregions and Arc-Expressing Ensembles in Active Place Avoidance Memory [Spatial Transcriptomics]
GEO Series GSE279273. Mus musculus. 2 samples. Type: Other.
Spatial transcriptomics reveal signatures of histopathological changes in muscular sarcoidosis
GEO Series GSE243291. Homo sapiens. 2 samples. Type: Other.
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.