Figure 6. Spatial reconstruction of single LECs using landmark genes obtained from pcRNAseq.
a-b) pcRNAseq-based zonation profiles of the panel of LEC landmark genes used to localize cells in the scRNAseq data. a) 70 pericentral LEC genes. b) 70 periportal LEC genes. Profiles were scaled between 0 and 1. c) Overlap of zonation profiles based on scRNAseq (blue) n=1163 single-cells and pcRNAseq (red) n=4602 paired-cells. Patches are s.e.m. Zonation profiles were normalized to their means across all layers (pcRNAseq profiles contain 8 layers whereas scRNAseq profiles contain 4). d) Ctsl (green dots) is highly expressed in hepatocytes (white dashed outline) and also expressed in the adjacent LECs (arrows). micrographs are representative of 10 lobules and two mice exhibiting similar results. e) scRNAseq spatial reconstruction reveals zonated expression of Ctsl in LECs, with a reduced expression level in pericentral LECs (1) compared to mid-lobule LECs (2). Box plot elements: center line, median; box limits, first to third quartile (Q1 to Q3) of the smFISH expression, horizonatal lines are medians. Quantification based on n= 30 cells from each layer from 2 mice. Gray patches mark the pericentral layers (CV, left) and periportal layers (PN, right). Blue is the scRNAseq-based zonation profile. Patches are s.e.m. Panels on the left show representative images. Blue is DAPI nuclear stain. Scale bar is 5μm in d)-e).