Extended Data Fig. 2: Accurate reconstruction of zonation patterns by trajectory inference.
a) scVI-integrated UMAP embedding of 0 and 2 dpi cells, discretized into five bins based on their position along the inferred trajectory. b) Expression levels of zonation markers defined by Moor et al. in each of the five discrete regions. To assess features at homeostasis, only 0 dpi cells were evaluated. Boxes range between the 25th and 75th percentiles, bars reflect the median, and whiskers extend 1.5x the interquartile range. c) Chromatin accessibility and expression evaluated at 0dpi for Tfrc, Slc2a2 and Slc15a1. Pseudo-bulk profiles of snATAC-Seq data associated with the indicated loci are plotted as genomic traces, along with the corresponding gene structure and peak identifications (left panels). Light grey bars highlight peaks with zonation-associated accessibility. Corresponding expression is shown to the right and colour coded according to pseudotime levels. For each gene, the height of ATAC traces was set to a common range and RNA expression quantified as log-transformed UMI counts per 10k counts (log CP10k + 1).
