Fig. 2: Comparison of FISHnCHIPs and single-molecule RNA FISH (smFISH) in mouse kidney tissue.
From: Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes
a Gene expression heatmap from the scRNA-seq reference data and their corresponding cell clusters. Heatmap shows expression of the 84 FISHnCHIPs genes that are correlated to the top differentially expressed (DE) genes in the 5 selected cell types, sampling a maximum of 300 cells per cluster. Cell type labels are distal convoluted tubule (DCT), loop of Henle (LOH), collecting duct principal cell (CD PC), collecting duct intercalated cell/collecting duct transitional cell (CD IC/Trans), proximal tubule (PT), unknown1, endothelial cell, podocytes, T-lymphocytes (T lymph), natural killer cell (NK), unknown2, fibroblasts (fib), macrophage, B lymphocytes (B lymph), neutrophil (neutro). b Unprocessed smFISH images of a mouse kidney tissue slice in 5 selected cell types are shown in the left and middle panels. FISHnCHIPs labels 14–23 co-expressed genes simultaneously to detect target cell types and their images are shown in the right panels. The smFISH and FISHnCHIPs images are scaled to the same camera intensity range for each cell type. Nuclei staining with DAPI is shown in blue. Scale bar, 3 μm. c Composite FISHnCHIPs image with each cell type assigned a pseudo color: endothelial (green), collecting duct (red), podocyte (magenta), loop of Henle (blue) and macrophage (yellow). Scale bar, 250 μm. Insert: Zoomed-in region of the white box. Scale bar, 25 μm. d–i Zoomed-in region of the white box insert in (c). Scale bar, 25 μm.
