Extended Data Fig. 1: scRNA-seq pre-processing.
From: Space-time logic of liver gene expression at sub-lobular scale
a, Histogram of number of UMIs per cell barcode for each mouse. Red patches mark the cells used for background estimation (100-300 UMI/cell barcode), gray patches mark the cells used for downstream analysis (1000-10000 UMI/cell barcode). b, Histogram of fraction of all UMIs mapping to mitochondrial genes. Filter used for downstream analysis in grey (0.09–0.35). c, smFISH staining of a liver lobule with probes against Cyp2e1 (red) and Cyp2f2 (green). CV = central vein, PN = portal node. Overall, the data combine 10 images from from two mice. d, Expression of Cyp2e1 and Cyp2f2 in cells with different fraction of mitochondrial expression. Three different filters for the fraction of UMIs mapping to mitochondrial genes (0–0.09, 0.09–0.35, 0.35–1) were applied, the data of all mice merged and the resulting datasets visualized as t-SNE plots. e, Violin plots for the correlations between Cyp2e1 and Cyp2f2 expression in single hepatocyte populations with different filters for fractions of mitochondrial expression. Each dot represents one mouse (n = 10 mice for each distribution) and the shape of the violin represents the density of points. f, Comparison of the zonation profiles of Z and Z + R genes obtained in our current study and the previous reconstruction from Halpern et al. 8. Profiles were interpolated to fit 15 layers, where 1 is pericentral and 8 is periportal. Dots indicate the center of mass (expression-weighted lobule layer) of the Z and Z+R genes computed in both datasets, for gene having an average expression of at least 10−5 in Halpern et al. r is the correlation coefficient, p the corresponding p-value from a standard linear regression.
