Fig. 3: Spatial location of Barrett’s esophagus cell types.
From: Clonal cell states link gastroesophageal junction tissues with metaplasia and cancer
a Schematic of the spatial transcriptomics workflow on fresh frozen sections of Barrett’s esophagus tissue. scRNA-seq data was integrated with highly multiplexed RNA FISH (seqFISH) to map cell types. b seqFISH of fresh frozen Barrett’s esophagus tissue for previously identified cell type markers from scRNA-seq (Fig. 2a, 2c); shown are a subset of marker genes. RNA Signal was called computationally and overlaid on DAPI images. DAPI staining is displayed in blue. Scale bars, 50 μm. c Annotation of the section from (b) with Barrett’s esophagus cell type markers from scRNA-seq; the colors match the labels in Fig. 2a and Fig. 3d. d Boxplot of distance to the lumen for all epithelial cells in (b) split by cell type. Boxplot shows the median, first and third quartiles, and 1.5 times the interquartile range below the first quartile and above the third quartile; outliers were removed. Data is shown for one region of interest (ROI) from one patient. Additional patients and ROIs are in Fig. S15.
