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Fig. 4 | Genome Biology

Fig. 4

From: Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference

Fig. 4

Case study of differential expression analysis of INF- β stimulated PBMCs using two matched pools that consist of 8 samples. a UMAP representation of single-cell transcriptome profiles, colored by eight major cell types identified. Note, M denotes Monocytes. b Analogous UMAP representation colored by the experimental condition: stimulated versus unstimulated. c The number of stimulated and unstimulated B cells sequenced in each of the 8 samples. df Differential gene expression (DE) analysis between stimulated and unstimulated B cells. d The expression level of an example gene OAZ1, depicting the distribution of expression levels in both conditions, either considering each sample separately (S1..S8) or considering aggregated data pooled across all samples (All). FDR: adjusted P value (Benjamini-Hochberg) of each DE test between conditions with likelihood-ratio test. CPM: count per million. e Number of recurrently detected DE genes between conditions (FDR <0.05), detected in at least one to eight samples. Box plots in gray show the recurrence expected by chance (based on 200 permutations). f The number of DE genes in each of the 8 samples, categorized by the number of recurrent DE discoveries across samples, that is the number of individuals in which a given gene is identified as DE (FDR <0.05)

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