Journal: Nature cardiovascular research

Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

doi: 10.1038/s44161-022-00138-1

Figure Lengend Snippet: Fig. 1 | Single-cell and spatial transcriptomics of cardiac and ileum tissue of reovirus-infected neonatal mice. a, Experiment and analysis workflow. Four- day-old neonatal mice weighing 3 g per pup were infected (per os) with reovirus T1L. Neonatal mice infected with 1× PBS were used as mock controls. Ileum tissue (1 dpi and 4 dpi) and heart tissues (4 dpi, 7 dpi and 10 dpi) were assayed and used for scRNA-seq and spatial transcriptomics. b, UMAP plot of 31,684 single-cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi (one animal per condition), clustered by gene expression and colored by cell type (left). UMAP plots showing cardiac cell type clusters across samples for the heart scRNA-seq data (right). c, 8,243 spatial transcriptomes of cardiac tissue sections from mock-infected and reovirus-infected mice at 4 dpi and 7 dpi (one animal per condition). H&E-stained image of reovirus-infected myocarditic

Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

Techniques: Infection, Gene Expression, Staining

Journal: Nature cardiovascular research

Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

doi: 10.1038/s44161-022-00138-1

Figure Lengend Snippet: Fig. 3 | Cytotoxic T cells recruited by inflamed endothelial cells induce pyroptosis in myocarditic tissue. a, UMAP plot of 9,786 single-cell endothelial cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by endothelial cell subtype clusters (phenotypes) (top) and condition (bottom). b, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for endothelial cell subtypes. c, UMAP plot showing the expression of genes upregulated in Cxcl9-high endothelial cells. d, Spatial transcriptomic maps of cardiac tissue from reovirus infected hearts at 7 dpi showing gene module scores calculated for four GO terms enriched in Cxcl9-high endothelial cells. e, UMAP plot of 2,205 single-cell T cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by T cell subtype clusters (top) and condition (bottom). f, Heat map showing top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for T cell subtypes. g, UMAP plot showing the expression of genes upregulated in cytotoxic T cells from myocarditic heart at 7 dpi. h, Spatial transcriptomics maps of cardiac tissue from reovirus infected hearts at 7 dpi

Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

Techniques: Infection, Expressing

Journal: Nature cardiovascular research

Article Title: Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

doi: 10.1038/s44161-022-00138-1

Figure Lengend Snippet: Fig. 4 | Myocarditic regions and the border zone have distinct transcriptomic profiles and cell-type-specific signatures. a, Spatial transcriptomics map of cardiac tissue section from reovirus-infected mice at 7 dpi colored by spot clusters representing transcriptionally distinct tissue regions. b, Spatial transcriptomics maps of cardiac tissue sections from reovirus-infected mice at 7 dpi showing the expression of differentially expressed genes of interest in the myocarditic and the border zone. c, Changes in average predicted cell type proportions across the infected ventricle, for cell types enriched in the myocarditic region and the border zone. d, UMAP plot of 502 single-cell cardiomyocyte cell transcriptomes from mock-infected and reovirus-infected hearts at 4 dpi, 7 dpi and 10 dpi colored by myocyte cell subtype (phenotypes) (left) and condition (right). e, Heat map showing the top five differentially expressed genes (two-sided Wilcoxon test, log fold change > 1.0 and P < 0.01) for cardiomyocyte cell subtypes. f, Venn diagram showing myocyte-specific genes

Article Snippet: UMAP plot showing the expression of myocyte-specific genes that are upregulated in the border zone of myocarditic regions (right). g, High-resolution Slide-seq spatial transcriptomics map of cardiac ventricular tissue from reovirus infected mice at 7 dpi colored by Slide-seq bead clusters.

Techniques: Infection, Expressing

Journal: Communications Biology

Article Title: SpatialPrompt: spatially aware scalable and accurate tool for spot deconvolution and domain identification in spatial transcriptomics

doi: 10.1038/s42003-024-06349-5

Figure Lengend Snippet: Shows the quantitative assessment result for domain identification using human dorsal prefrontal cortex (DLPFC) and Slide-seq dataset

Article Snippet: The spatial Slide-seq dataset and the corresponding scRNA-seq retrieved from the Broad Institute single-cell portal ( https://singlecell.broadinstitute.org/single_cell/study/SCP948/robust-decomposition-of-cell-type-mixtures-in-spatial-transcriptomics ).

Techniques: