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Fig. 6 | Genome Biology

Fig. 6

From: Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2

Fig. 6

Joint analysis of single-cell RNA and protein data. a The number of unique barcode reads per mRNA or ions per peptide/protein for the set of 2383 genes detected in both datasets. Peptides and proteins were filtered to 1% FDR. Proteins from genes not quantified in the RNA data were omitted and vice versa. The higher copy numbers measured for proteins support more reliable counting statistics compared to mRNAs. b Distributions of correlations between ri and pi, where ri is the vector of pairwise correlations of the ith RNA to all other RNAs, and pi is the vector of pairwise correlations of the ith protein to all other proteins [13, 40]. The null distribution corresponds to permuting the order of RNAs and proteins. The two modes of the distribution of correlations for all genes were used to define gene clusters 1 and 2. The correlations between pi and ri were then recomputed just within the space of genes from clusters 1 or from clusters 2 and displayed as separate distributions. c Genes from cluster 1 display similar abundance profiles at both the RNA and protein levels, while genes from cluster 2 display the opposite profiles. The columns correspond to single cells ordered by the first common principal component (CPC 1), which strongly correlate to cell type both for the RNA and for the protein dataset. Cluster 1 genes are ordered by the left CPC 1, and cluster 2 genes by the fold change across the ordered cells from both RNA and protein datasets. df Joint projections of the RNA and protein data by Conos [41]. d Cells analyzed by SCoPE2 are color-coded by cell type while cells analyzed by scRNA-seq are marked gray. e All single cells are color-coded by biological replicate and batch. f Cells are color-coded by the expression of marker genes for monocytes and macrophages

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