Figure 5. Statistical analysis of single-cell multiplexed error-robust fluorescence in situ hybridization (MERFISH) and Tabula Muris Senis RNA count distributions.
(A, B) Comparison of mean RNA counts in MERFISH versus scRNA-seq in mouse (A) liver and (B) kidney across cells with nonzero counts. Each dot represents a gene, and only genes possessing at least 50 cells with nonzero counts are shown for each tissue. The dotted black line shows the x = y line, indicating one-to-one concordance between MERFISH and scRNA-seq. (C, D) Mean–variance relationship for RNA counts in MERFISH (blue) and scRNA-seq (orange) for the mouse (A) liver and (B) kidney, across cells with nonzero counts. Each dot represents a gene, and only genes possessing at least 50 cells with nonzero counts are shown for each tissue. The dotted line indicates the x = y line, which represents the Poisson scenario where the mean equals the variance. (C, inset) Distribution of MERFISH RNA counts across cells with nonzero counts for Hmgcs2, a liver hepatocyte marker gene. The red line indicates the best fit to a negative binomial distribution. (D, inset) Distribution of MERFISH RNA counts across cells with nonzero counts for Kcnj1, a kidney loop-of-Henle cell marker gene. Red line indicates the best fit to a negative binomial distribution. Error bars in (A) and (B) represent the standard error of the mean.