Fig. 5: snRandom-seq discovered a proliferative subpopulation in the clinical FFPE human specimen. | Nature Communications

Fig. 5: snRandom-seq discovered a proliferative subpopulation in the clinical FFPE human specimen.

From: High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq

Fig. 5

a Experimental overview of clinical FFPE sample of human macrotrabecular-massive hepatocellular carcinoma (MTM-HCC) subtype for snRandom-seq. b Histological appearance of MTM-HCC at low magnification (left, Scale bar, 5 mm.) and high magnification (right, Scale bar, 200 μm). Red dashed circle: tumorous area. Blue dashed circle and line: sampling area. White dashed circle and line: magnified area. c Violin plots and box plots showing the number of genes and UMIs detected in FFPE clinical human sample by snRandom-seq. MTM-HCC nuclei: n = 5914. Data was presented as median values. Data in the box plot corresponded to the first and third quartiles (lower and upper hinges) and median (center). Data in the box plot corresponded to the first (lower hinges) quartiles, third quartiles (upper hinges), and median (center). The upper whisker extended from the hinge to the maxima no further than 1.5 * IQR from the hinge. The lower whisker extended from the hinge to the minima at most 1.5 * IQR of the hinge. d t-SNE map of nuclei isolated from the FFPE sample based on their gene expressions. Six cell types, including two hepatocellular subtypes, were annotated and shown. e Top three markers of each of the six cell types. f Percentages of the nuclei in phase G1, G2M, or S in the six cell types. g The total number of interactions among different cell populations. Circle sizes represented the number of cells in each cell group and edge width represented the communication probability. h The heatmap showing the outgoing signaling patterns (left) and incoming signaling patterns (right) of each cell cluster. i Bubble diagrams showing the communication probability and statistical significance of receptor-ligand pairs in BMP signaling network. Dot color represented communication probabilities and dot size represented computed p values. Empty spaces mean that the communication probability was zero. p-values were computed from one-sided permutation test. Source data are provided as a Source Data file.

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