array-based spatial transcriptomics visium 10x  (Spatial Transcriptomics Inc)

Journal: Nature Communications

Article Title: Host-pathogen interactions in the Plasmodium -infected mouse liver at spatial and single-cell resolution

doi: 10.1038/s41467-024-51418-2

Figure Lengend Snippet: a Schematic representation of the experimental design of this study. Livers were collected at 12, 24, or 38 h post infection (hpi) with P. berghei parasites or salivary gland lysate of uninfected mosquitoes (SGC) (left). Immunofluorescence (IF) staining of the parasite, spatial transcriptomics (ST) or 10X visium spatial technology protocols, and droplet-based single-nuclei RNA sequencing (snRNA-seq) were performed (center). Both data were further analyzed computationally (right). IHS stands for immune hotspot. b After dimensionality reduction, the normalized and batch-corrected data were embedded in UMAP space and split by the original condition for visualization. Data from SGC sections are shown on the top from 12 to 38 hpi (left to right) and data from P. berghei - infected sections are shown on the bottom from 12 to 38 hpi (left to right). Clusters with an obvious association to infection conditions are highlighted with gray boxes. c For identified clusters ST10 and ST11, differential gene expression analysis (DGEA) was performed, followed by functional enrichment analysis for each cluster (see Methods for details). Overrepresented pathways of the KEGG database for ST10 are shown in rose and for ST11 in aquamarine. Scales for expression values of overrepresented genes belonging to the individual KEGG pathways are shown for ST11 (left) or ST10 (right), from high expression (dark) to lower expression (light). Selected gene names are shown at the bottom. Enrichment scores for the pathways are shown on the right. d Interaction analysis of clusters was performed to evaluate spatial enrichment expression programs as suggested by clustering analysis in space. Positive enrichment values (orange) indicate spots belonging to these clusters are more likely to be neighboring, while negative enrichment values (blue) indicate spots associated with these expression programs are less likely to be neighboring. Clusters without significant enrichment in each other’s neighborhoods are shown in white. e Visium clusters were imposed on spatial positions and annotated according to spatial expression features. Sections of the investigated conditions are divided for ease of inspection as in ( b ), with the top panel comprising SGC sections across 12–38 hpi and the bottom panel comprising P. berghei infected sections across 12–38 hpi.

Article Snippet: In this study, we use a combination of the original Spatial Transcriptomics 2K arrays , (henceforth referred to as ST) and Visium arrays (10X Genomics Inc.) .

Techniques: Infection, Immunofluorescence, Staining, RNA Sequencing, Gene Expression, Functional Assay, Expressing