Fig. 4: Spatial transcriptomic with MicroCart. | Nature Communications

Fig. 4: Spatial transcriptomic with MicroCart.

From: A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment

Fig. 4

A Left: Illustration of the validation scheme for bacteria probes on the BMAs, using MicroCart-DSP spatial sequencing as a readout. Right: Barplots showing sequencing counts (mean ± 0.95 CI) from the respective probes in different bacteria species arrays (From 6 ROIs for each species). Red dotted line indicates the limit of detection. Created in BioRender. Zhu, B. (2024) https://BioRender.com/h69v030. B Violin plot showing the bacteria probe signal levels (summed within each bacterial ROIs), and compared across tissue types and treatment types. Firm: Firmicutes; Bac: Bacteroidetes; Pro: Proteobacteria; PAN: all bacteria. ROI numbers for each group: Ctrl - Large: 20; Ctrl - Small: 17; DSS - Large: 45; DSS - Small: 26. The box plot indicates 25–75 percent quantiles (box boundary), medium values (line in box), and min/max values (whiskers). C Volcano plots showing top differentially expressed genes for host cells between healthy and colitis samples, separated by MicroCart-DSP region compartments (E-Cad+ or CD45+) and tissue locations. D GSEA analysis showing the top 15 enriched gene pathways in the colitis groups, separated by MicroCart-DSP region types and tissue locations.

Back to article page