visium formalin-fixed, paraffin-embedded spatial transcriptomics analysis  (Spatial Transcriptomics Inc)

Journal: bioRxiv

Article Title: Multi-modal refinement of the human heart atlas during the first gestational trimester

doi: 10.1101/2024.11.21.624698

Figure Lengend Snippet: ( A ) Samples of nuclei were derived from three whole dissociated hearts to generate distinct single-cell RNA-seq datasets at 8.6 post-conceptional weeks (pcw, confirmed XX genotype), 9.0 pcw (XY) and 10.7 pcw (XY). Samples of spatial transcriptomic analysis were derived from two whole dissociated hearts to collect cryosections and generate Visium datasets at 8.4 pcw (XY, 2 sections) and 9.7 pcw (XX, 4 sections). ( B ) Integrated UMAP representation of 49,227 profiled nuclei coloured by cell type. ( C ) UMAP representation of profiled nuclei as in (B) but separated by sample. Arrows indicate cluster 12 (SMC) in each, but that all cell types are present at each sample. ( D ) UMAP plots per sample indicating that all cell classes are also represented in each sample. ( E ) Dot plot of top marker genes for each Class (y axis: cardiomyocytes (I), endocardiovascular cells (II), stroma (III), epicardium (IV), blood (V) and neural crest progeny (VI). The size of the dot represents the percent of nuclei with transcripts at non-zero levels, and color intensity represents average log-normalized expression of the gene where relative abundance of typical markers is indicative of cell class. ( F ) UMAP feature plots of representative gene expression in Classes I to VI for MYH7 (cardiomyocytes), PECAM1 (endothelial and endocardial cells), EBF2 (stroma), TBX18 (epicardium), SPP1 (immune cells) and NRXN1 (neural crest). ( G ) Heatmap showing selected genes expressed in the nine cardiomyocyte clusters of Class I compared with the minority populations of lymphatic endothelium, Schwann cell precursors and neuroendocrine cells. Each column displays gene expression of an individual cell and genes are listed in the rows.

Article Snippet: As transcriptomics of single nuclei is high-resolution but sparse, and removes informative positional information from samples, we also undertook 10x Genomics Visium spatial transcriptomics analysis on two sections from a male heart collected at 8.4 pcw and four sections from a female one at 9.7 pcw ( , Figs. S4-9).

Techniques: Derivative Assay, RNA Sequencing Assay, Marker, Expressing

Journal: bioRxiv

Article Title: Multi-modal refinement of the human heart atlas during the first gestational trimester

doi: 10.1101/2024.11.21.624698

Figure Lengend Snippet: ( A ) Seurat UMAP (Uniform Manifold Approximation and Projection) plot of integrated spatial transcriptomic data from two 8.4 postconceptional week (pcw) heart sections and four 9.7 pcw heart sections. Each dot represents a spot covered by a histological section on the Visium spatial capture slides. 14 clusters of the developing heart corresponding to cardiac cell types are listed. ( B ) Visualization of clustering on each heart section after integration of spatial transcriptomic data. Cluster annotations and colors match those of the UMAP in A. ( C ) Spatial plots showing gene expression on heart sections, with highest expression in red and lower expression in blue. RV, right ventricle; LV, left ventricle; RA, right atrium; LA, left atrium; Ao, aorta.

Article Snippet: As transcriptomics of single nuclei is high-resolution but sparse, and removes informative positional information from samples, we also undertook 10x Genomics Visium spatial transcriptomics analysis on two sections from a male heart collected at 8.4 pcw and four sections from a female one at 9.7 pcw ( , Figs. S4-9).

Techniques: Expressing