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Fig. 2 | BMC Biology

Fig. 2

From: Single-cell RNA sequencing of the retina in a model of retinitis pigmentosa reveals early responses to degeneration in rods and cones

Fig. 2

Pseudotime analysis of rod transcriptomes. Rod cells on the recalculated principal component analysis plot were colored according to A cluster identity or B pseudotime values (alongside the single principal curve). C Violin plots of pseudotime values in each rod cluster. Significance of pseudotime differences in each cluster was tested with one-way ANOVA and Tukey’s range test. ***p-value < 2e−16. D Rods were grouped into 16 bins according to their pseudotime values. Top: Histogram for rod cell counts from each cluster in each pseudotime bin (x-axis)). Bottom: Differential gene expression analyses between clusters adjacent in pseudotime were used to build differentially expressed (DE) gene sets (adjusted p-value < 0.05). For each DE gene, average scaled expression (z-score) values in each pseudotime bin were used to cluster genes according to their pseudotemporal expression pattern (k-means clustering, k = 4). Vertical red bars mark positions in pseudotime where cells’ cluster identities change

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