Extended Data Fig. 8. Spatial mapping of whole transcriptome and epigenome.
a, Imputed mRNA expression of ALD1 (Top) predicted its mRNA expression pattern measured with MERFISH (Bottom). Magnified images are shown on the right. b, Imputed mRNA expression of ICS1 (Top) predicted its mRNA expression pattern measured with smFISH (Bottom). Magnified images are shown on the right. c, Imputed ATAC activity (Extended Data Fig. 5f) of ICS1 (top) and ALD1 (bottom), which showed consistent patterns with mRNA expression (a,b). d, Imputed motif enrichment scores of HsfB2b (Top) was consistent with mRNA expression of HsfB2b confirmed by MERFISH (Bottom). e, Spatial mapping of pseudotime values based on data integration and label transfer between snRNA-seq and MERFISH data of DC3000-infected plants. f, smFISH of ICS1 in leaves infected by AvrRpt2 or DC3000 at 24 hpi. g, Spatial mapping of bacterial transcripts detected with smFISH in plants infected by AvrRpt2 (left) and DC3000 (right) at 24 h post-infection (hpi). Pseudotime values are also visualized in the background. Dot size reflects the number of bacterial transcripts detected. a-g, Scale bars = 1 mm. h, Scatter plot showing the number of bacterial transcripts (x-axis) and averaged pseudotime values of five nearest neighbor plant cells (y-axis) for each bacterial colony in plants infected by AvrRpt2 (blue) and DC3000 (red) at 24 hpi. i, Averaged pseudotime scores of cells surrounding each bacterial colony. The x-axis shows the number of nearest plant cells analyzed for each bacterial colony. Shaded error bands indicate standard error of the mean.