Fig. 5: SpotClean improves marker specificity in human pancreatic cancer12 sample PDAC-A.
From: SpotClean adjusts for spot swapping in spatial transcriptomics data
a H&E image (left) and spots annotated as tumor, duct epithelia, pancreatic tissue, and stroma from the original study (right). Scale bar is 1 mm. b The upper panel shows expression of the tumor-specific marker TMSF1 in the raw (left) and SpotClean decontaminated (right) data. SpotClean increases specificity of this marker by maintaining expression in the tumor region, and reducing expression in the non-tumor regions. A pancreatic-specific marker, PRSS1, is shown in the lower panel; as in the upper panel, the specificity of this marker is increased via SpotClean. c UMAP plots generated from raw and SpotClean decontaminated data colored by spot annotations (tumor vs. non-tumor). The groups are well separated even in the raw data, but SpotClean decontaminated data leads to slightly improved separation of the groups.
