Fig. 5: Exon coordination patterns are observable across multiple cell types.
From: Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue
a, Pie chart of number of cell types where an exon pair is significant given significance in pseudo-bulk. b, Bar plot of percentage of tested exon pairs (one per gene) that were significantly coordinated. Cell type on the x axis (n = 98, 121, 101, 70 and 33). c, Bar plots of percentage of genes that are not testable in any cell type because at least one exon became constitutive. x axis values indicate adjacent (n = 114) or distant (n = 23). d, Bar plots of percentage of genes that are not testable in specific cell types because at least one exon became constitutive, colored by adjacent (n = 31, 31, 26, 26 and 22) or distant (n = 15, 15, 15, 15 and 14) exon pairs. e, Bar plot showing percent of distant coordinated exon pairs split by ASD association (n = 67 and 241). P value obtained from two-sided Fisher’s exact test. b–e, Error bars indicate s.e. of the point estimate. f, Distantly coordinated exons for the PTK2 gene. Each horizontal line indicates one transcript, colored by cell type; clustered blocks indicate exons. Gray denotes annotated GENCODE transcripts. Blue boxes highlight coordinated exons, labeled Alt. exon 1 and Alt. exon 2. Control exon for qRT–PCR highlighted in blue. g, Heat map showing exon pairs that were testable in at least one cell type (n = 127). Exon pairs colored by significant coordination in same (pink) or opposite (blue) direction as pseudo-bulk, not significant (white), not testable in a particular cell type because of low counts (gray) or exons becoming constitutive (teal). h, Box plots of the |log-odds ratio| of excitatory neuron reads for tested exon pairs versus the minimum PhastCons score being <0.5 (n = 26) or >0.5 (n = 93). i, Box plots of the ratio of double inclusion of an exon pair to coordination (for excitatory neurons). x axis same as in h. For box plots: center line, median; box limits, upper and lower quartiles; and whiskers, 1.5× interquartile range. P values (h, i) calculated using the two-sided Wilcoxon rank-sum test. Significance: *P < 0.05; **P < 0.005; ***P < 0.001; NS, not significant. Astro, astrocyte; EN, excitatory neuron; IN, inhibitory neuron; Oligo, oligodendrocyte.
