Fig. 3

Identifying differentially expressed isoforms between cell types using clustered single-cell data. A Workflow of differentially expressed isoform identification. R2C2 reads are separated by cell type, then used to identify and quantify isoforms. Genes with differential isoform usage between cell types are then identified using chi-squared tests. B–D Genome Browser shots of three genes with differential isoform expression. Gene annotation is shown on top. Isoforms as determined by Mandalorion on the entire dataset are shown below (“top strand” = blue, “bottom strand” = yellow). Relative quantification (%) of each isoform in each cell type and replicate is shown on the right. Isoforms with the most variable changes in abundance are indicated with a red arrow. For AIF1, we also include a refTSS track