Fig. 4: Analysis of 951 single-cell nanopore transcriptomes from a mouse E18 brain.

a 2D UMAP embedding from PCA performed jointly on variable gene and transcript features. Gradient coloring by pseudotime according to each trajectory. Neural Progenitor Cells are abbreviated Pro., Immature neurons Imm. and Mature neurons Mat. T1 and T2 describe the two trajectories of Glutamatergic neurogenesis observed. b Heatmap of significant AS events colored by the ratio of observed CSI vs. permuted CSI for permutations within (top) or across all (bottom) trajectories. c UMAP density column from top to bottom: Celf2 gene expression, Celf2 alternative 5′ splice site (A5) in intron 12 (Celf2:i12:A5, chr2:6560659-6560670; row highlighted in panel b), and juxtaposed alternative 3′ splice site (A3) for intron 12 (Celf2:i12:A3, chr2:6553965-6553982). d AS event diagram on the top of Celf2 gene intron 12 where exons are shown as boxes and introns as lines, with the A5 event in red, and the A3 event in blue, with reads from cells in the beginning and the end of the glutamatergic T1 trajectory shown below respectively (boxed regions from the bottom panel). In the bottom panel are plots of CSI for windows along pseudotime for the observed data (A5, red) and (A3, blue) plotted over the background permutations in gray. e Mean PSI values of sample group quantifications from the human (Hsa38, left) and mouse (Mmu10, right) VastDB splicing databases³⁰. Standard error is provided as bars (for sample groups with n > 1 samples), with source accession identifiers for each sample provided in Supplementary Data 2 and raw values in Source Data.