Fig 2: High-dimensional single-cell analysis of human pancreatic cancer sample with t-CyCIF.(A) t-SNE plots of cells derived from small intestine (left) or the PDAC region (right) of the specimen shown in Figure 7 with the fluorescence intensities for markers of proliferation (PCNA and Ki67) and signaling (pERK and ß-catenin) overlaid on the plots as heat maps. In both tissue types, there exists substantial heterogeneity: circled areas indicate the relationship between pERK and ß-catenin levels in cells and represent positive (‘a’), negative (‘b’) or no association (‘c’) between these markers. (B) Representative frames of normal pancreas and pancreatic ductal adenocarcinoma from the 8-cycle t-CyCIF staining of the same resection specimen from Figure 7. (C) t-SNE representation and clustering of single cells from normal pancreatic tissue (red), small intestine (blue) and pancreatic cancer (green). Projected onto the origin of each cell in t-SNE space are intensity measures for selected markers demonstrating distinct staining patterns. (D) Fluorescence intensity distributions for selected markers in small intestine, pancreas and PDAC.10.7554/eLife.31657.026Figure 8—source data 1.Single-cell data in FCS format (Figure 8C–E).

Fig 3: t-CyCIF imaging of normal tissues.(A) Selected images of a tonsil specimen subjected to 10-cycle t-CyCIF to demonstrate tissue, cellular, and subcellular localization of tissue and immune markers (see Supplementary file 1 for a list of antibodies). (B) Selected cycles from (A) demonstrating sub-nuclear features (Ki67 staining, cycle 1), immune cell distribution (cycle 2), structural proteins (E-Cadherin and Vimentin, cycle 5) and nuclear vs. cytosolic localization of transcription factors (NF-kB, cycle 6). (C) Five-cycle t-CyCIF of human skin to show the tight localization of some auto-fluorescence signals (Cycle 0), the elimination of these signals after pre-staining (Cycle 1), and the dispersal of rare cell types within a complex layered tissue (see Supplementary file 1 for a list of the antibodies).