Fig. 2

Fig. 2 Comparison and evaluation of ten chemical conversion methods using ZF4 cells.

a Box plot showing T-to-C substitution rates across control and ten chemical conversion methods in 4sU-labeled ZF4 cells. “Ctrl” denotes the untreated control group (n = 7531 cells). The ten chemically treated groups, from left to right, contain: n = 1587, 789, 5581, 5267, 4692, 4639, 5360, 6461, 5389, and 5233 cells. Box plots show the median (center line), interquartile range (box), 1.5× interquartile range. Source data are provided as a Source Data file. b, c Scatterplots comparing the number of genes (b) or UMIs (c) detected per cell as a function of aligned reads per cell across the ten chemical conversion methods. Color indicates treatment methods. Fitted lines for each method are included, along with the predicted number of genes or UMIs detected per cell at a sequencing depth of 10,000 reads. In (b), the curve is smoothed using locally weighted regression (LOESS), while in (c), a linear model (LM) is applied. The estimated numbers of genes or UMIs at 10,000 reads are displayed on the right of the figure. Source data are provided as a Source Data file. d Uniform Manifold Approximation and Projection (UMAP) visualization showing integrated control and datasets from the ten chemical conversion methods, representing 52,529 ZF4 cells. Cells are colored by cell type. The numbers of cells in each group are also indicated. e Visualization of unique transcripts (UMIs) of the cell-cycle gene tubb4b from individual ZF4 cells in the control group and across the ten chemical conversion methods. Grey circles represent uridines without T-to-C substitution, while crosses (“X“s) indicate uridines with T-to-C substitutions in at least one read. The read coverage for each T-to-C substitution is displayed with color scaling.