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. 2022 Oct 20;17(11):2531–2547. doi: 10.1016/j.stemcr.2022.09.010

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© 2022 The Author(s)

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

PMC Copyright notice

Transcriptomic comparison of iHSCs, qHSCs, pHSCs, and fibroblasts

(A) Representative heatmap of transcriptomic profiles of endoderm-derived iHSCs (iHSCs_end, n = 3) and mesoderm-derived iHSCs (iHSCs_M2, n = 3), purchased primary HSCs (purHSCs, n = 3), primary HSCs isolated from liver tissue (pHSC, n = 3), quiescent HSCs (qHSCs, n = 8) (GSE141100), iPSC-derived qHSCs (TkDN4_M_qHSCs, n = 3, and FF_1_qHSCs, n = 3) (GSE155017), human hepatocytes (hep, n = 1) (GSE43984), cultured hepatocytes (cul_hep, n = 2, GSE98710), and fibroblasts (n = 3).

(B) PCA of the transcriptomic comparison of endoderm-derived iHSCs (iHSCs_end, n = 3) and mesoderm-derived iHSCs (iHSCs_M2, n = 3), purchased primary HSCs (purHSCs, n = 3), primary HSCs purified from liver tissue (pHSC, n = 3), quiescent HSCs (qHSCs, n = 8) (GSE141100), iPSC-derived qHSCs (TkDN4_M_qHSCs, n = 3, and FF_1_qHSCs, n = 3) (GSE155017), human hepatocytes (hep, n = 1) (GSE43984), cultured hepatocytes (cul_hep, n = 2, GSE98710), and fibroblasts (n = 3).

(C) Heatmap of the top 500 HSC genes expressed differently in endoderm-derived iHSCs (iHSCs_end, n = 3) and mesoderm-derived iHSCs (iHSCs_M2, n = 3), purchased primary HSCs (purHSCs, n = 3), primary HSCs purified from liver tissue (pHSC, n = 3), quiescent HSCs (qHSCs, n = 8) (GSE141100), iPSC-derived qHSCs (TkDN4_M_qHSCs, n = 3, and FF_1_qHSCs, n = 3) (GSE155017), human hepatocytes (hep, n = 1) (GSE43984), cultured hepatocytes (cul_hep, n = 2, GSE98710), and fibroblasts (n = 3).

(D) GSEA of the iHSC gene expression profile with qHSC and aHSC (GSE141100) gene signatures according to the phenotype described. NES, normalized enrichment score.

(E) GO analysis of 959 high-fold-change genes between iHSCs_end and TkDN4_M_qHSCs (GSE155017). The p values of the top 20 terms are indicated.

(F) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 959 high-fold-change genes between endoderm-derived iHSCs (iHSCs_end) and other iPSCs derived qHSC-like cells from another laboratory (TkDNA4_M_qHSCs, GSE155017). The p values of enriched pathways are indicated. Data are represented as the mean ± SEM. See also Table S1.