Extended Data Figure 9: Similarities and differences between endothelial and MCs from the LB and primary human liver.

a, For each cell, the similarity to either mock-bulk RNA-seq data from input MSCs grown in 2D culture or primary stellate cells from the fetal liver was calculated using quadratic programming and plotted as fractional identities (left axis, circle, fractional MSC 2D identity; right axis, triangle, fractional stellate identity). Points are coloured on the basis of the experiment: input MSCs in 2D (MSC, light green), MSCs from early LB (MSC-LB early, red), MSCs from late LB (MSC-LB late, purple), primary fetal stellate (fetal stellate, green). b, Heatmap shows normalized correlation (z-score) of single-cell transcriptomes with mock-bulk RNA-seq data from MSCs from early stage LBs, MSCs from late stage LBs, MSCs grown in 2D, and fetal stellate cells. c, tSNE clustering of mesenchymal and stellate cells on the basis of genes identified using PCA. This analysis was used to identify genes specific to fetal stellate cells (Supplementary Table 5). d, Violin plots showing the expression distributions of genes similarly and differentially expressed between MSC-LB and fetal stellate cells. White circle, mean. e, For each cell, the similarity to either mock-bulk RNA-seq data from input ECs grown in 2D culture or primary ECs from fetal and adult liver was calculated using quadratic programming and plotted as fractional identities (left axis, circle, fractional EC 2D identity; right axis, triangle, fractional primary EC identity). Points are coloured on the basis of the experiment: input ECs in 2D (EC, green), ECs from early LB (EC-LB, red), and primary fetal and adult ECs (primary EC, red). f, Heatmap shows normalized correlation (z-score) of single-cell transcriptomes with mock-bulk RNA-seq data from ECs grown in 2D, ECs from early stage LBs, and primary liver ECs. g, tSNE clustering of ECs on the basis of genes identified using PCA. This analysis was used to identify genes specific to primary liver ECs (Supplementary Table 5). h, Violin plots showing the expression distributions of genes similarly and differentially expressed between EC-LB and primary endothelial cells. White circle, mean.