Extended Data Fig. 4: Slide-seq predicted cell types.
From: An atlas of healthy and injured cell states and niches in the human kidney
a. UMI counts per bead for classified beads. Normalized RCTD weights for the beads classified at subclass level 2 (Methods). Region of the tissue associated with beads for each subclass. Frequency of cell types predicted across pucks. b. Dot plot showing expression of cell type markers identified by snCv3 in the classified Slide-seq beads. c. Representative pucks showing subclass level 2 classifications. Cell types are grouped into 3 categories and plotted separately for clarity. Scale bar is 300 µm. d-e. Cell proximity networks for Slide-seq cell types associated with cortical or medullary regions. For panels a, b, d and e all pucks (6 individuals) were combined. f. Left panel: Slide-seq puck area indicated in (c) and predicted cell types for the AEAs and surrounding cell types. Right panel: mapped expression values for corresponding marker genes (scaled). AEA mapping over Visium histology is depicted in Extended Data Fig. 5j, colocalized with REN expression. Scale bar is 100 µm.
