Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2024 Jan 5;26(1):153–167. doi: 10.1038/s41556-023-01316-4

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Extended Data Fig. 3 — a. Pseudobulk chromatin profiles at different gene loci for LSEC zonation states, accompanied by violin plots representing the normalized gene expression of the relevant gene in each class. UMAPs show the gene expression of the relevant genes with RGB encoding. b. Normalized region accessibility and gene expression zonation heat maps. LSECs are ordered by pseudotime (from periportal to pericentral) and regions and genes affected by zonation are shown (281 regions and 220 genes). c. GAM fitted gene expression profiles for selected genes along the zonation pseudotime for LSECs. d. Liver section image showing smFISH profiles for Ntn4 (PP LSEC marker) and Kit (PC LSEC marker). e. ScoMAP liver lobule and smFISH coloured by gene expression using RGB encoding. f. Pseudobulk chromatin profiles at different gene loci for HSC zonation states, accompanied by violin plots representing the normalized gene expression of the relevant gene in each class. UMAPs show the gene expression of the relevant genes with RGB encoding. g. Normalized region accessibility and gene expression zonation heat maps. HSCs are ordered by pseudotime (from periportal to pericentral) and regions and genes affected by zonation are shown (475 regions and 275 genes). h. GAM fitted gene expression profiles for selected genes along the zonation pseudotime for HSCs. i. Liver section image showing smFISH profiles for Ntgr (HSC PP marker) and Adamtsl2 (PC HSC marker). j. ScoMAP liver lobule and smFISH coloured by gene expression using RGB encoding. For the transcriptome and epigenome data, cells from 5 and 4 biological replicates were combined, respectively. For i and h, three independent experiments were performed, with similar results. HSC: hepatic stellate cells, LSEC: liver sinusoidal endothelial cells, PC: pericentral, PP: periportal. Source numerical data are available in source data.

Source data