Figure 3. Variation in isoform usage between single cells.
a, RNA-Seq read densities in single cells (blue) and population replicates (grey) for two illustrative loci, each with two different isoforms (bottom). b, Distributions of exon inclusion (PSI scores, X axis) for alternatively spliced exons of highly expressed genes (single-cell TPM > 250) in individual cells (blue histogram, top) and populations (grey histogram, bottom). c, Left: RNA-Seq read densities for Irf7 (only cells where the transcript is expressed are shown). Colored boxes mark exons analyzed by RNA-FISH. Right: RNA-FISH images from simultaneous hybridization with probes for two constitutive (‘Con’) regions of the transcript (A: cyan (C); B: magenta (M)) and one alternatively spliced exon (‘Specific’: orange (O)). White arrows (middle panel) highlight two cells with high levels of Irf7, but opposite preferences for the alternatively spliced exon. Histograms showing global abundance ratios for isoform-specific and constitutive probes (cells with less than 5 constitutive counts have been excluded; n = 490 cells; bottom histogram deviates from 0.5 due to probe design, see SI).