Extended Data Fig. 5: Spatial transcriptomic profiles of two HCC samples by Stereo-seq.
a, The number of genes captured by Stereo-seq at 10–200 bin resolutions. b, The number of transcripts captured by Stereo-seq at 10–200 bin resolutions. c, The DAPI fluorescence images (left), H&E staining images (middle) and number of genes detected at 100 bin resolution (right) of HCC01 (upper) and HCC03 (bottom). No replicates for these micrographs. d, Spatial visualization of onco-fetal markers FOLR2, PLVAP and POSTN in HCC01 analyzed by Stereo-seq at bin 100 resolution. e, Spatial visualization of onco-fetal cells in HCC01. The bins enriched with onco-fetal cells are highlighted with red. f, Spatial visualization of expression of indicated genes in HCC01 (upper) and HCC03 (bottom) at bin 100 resolution. g, Boxplot showing the expression of POSTN+ CAF signature in bins with different enrichment patterns of PLVAP+ EC or FOLR2+ TAM1 in HCC01. PLVAP+ EC low, n = 29,964 bins; PLVAP+ EC high, n = 6,812 bins; FOLR2+ TAM1 low, n = 29,649 bins; FOLR2+ TAM1 high, n = 7,127 bins. h, Bubble heatmap showing expression of POSTN+, POSTN- and panCAF signature genes in different CAF subsets. Dot size indicates the fraction of expressing cells, colored according to z-score normalized expression levels. i, Spatial visualization of selected cluster signatures in HCC03 analyzed by Stereo-seq at bin 100 resolution. j, Boxplot showing the expression of POSTN- and panCAF signature in bins with different enrichment patterns of PLVAP+ EC or FOLR2+ TAM1 in HCC03. PLVAP+ EC low, n = 19,905 bins; PLVAP+ EC high, n = 4,036 bins; FOLR2+ TAM1 low, n = 20,013 bins; FOLR2+ TAM1 high, n = 3,928 bins. For c-f and i, HCC01, n = 36,776 bins; HCC03, n = 23,941 bins. For g and j, Center line indicates the median value, lower and upper hinges represent the 25th and 75th percentiles, respectively, and whiskers denote 1.5× interquartile range. *P < 0.05, **P < 0.01, ***P < 0.001. Two-sided Wilcoxon test. Spatial cross-correlation test.
