a–d, Histograms of the expression distributions of genes measured by smFISH (left) and scRNA-seq (right) for genes: Hdac6 (a), Msl3 (b), Mpp1 (c) and Igbp1 (d). The number of cells quantified for each gene, cell type and method is presented above each figure item. e, f, Scatter plots of burst size (e) and frequency (f) inferred based on data from scRNA-seq and smFISH. Data from both fibroblasts and ES cells are shown. Although the few data points do not allow for a systematic comparison between methods, we observed a few trends. There was a good agreement for both burst size and frequency except for the gene Igbp1 that is an outlier in both scatterplots. Igbp1 has increased burst size and lower burst frequency in scRNA-seq than in smFISH. Excluding Igbp1, we see a fairly linear correspondence between methods over the remaining six data points (three genes and two cell types). g–j, Point estimates and confidence intervals shown for each gene, cell type and method based on the profile likelihood method. Number of cells used for the inference is shown in the corresponding histogram in a–d. P values for cell-type comparison in burst kinetics is shown per method based on the profile likelihood test.