Fig. 3: snPATHO-seq detected comparable transcriptomic signatures from FFPE samples as the conventional Flex chemistry using matching snap-frozen samples.
From: snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives
a Heatmap showing similarities between robust NMF programs derived from snPATHO-seq, 10x 3’, and 10x Flex data generated using 4066, 4399, and 4411. Robust NMF programs with similar gene compositions were clustered and highlighted in brackets. b Table of robust NMF program clusters annotated based on the shared gene compositions. c UMAP embedding of Seurat CCA integrated data from patients 4066 (i–iii), 4399 (iv–vi), and 4411 (vii–ix) overlaid with the expression of MKI67 (i, iv, vii), the module scores of robust NMF program cluster C6 (ii, v, viii) and the module scores of a published cell cycle gene program23 (iii, vi, ix). d Spatial enrichment pattern of the module score of robust NMF program cluster C3 in the Visium data from patient 4066 and the H&E image of this sample. Scale bar = 1 mm.
