Extended Data Fig. 4: Reproducibility and quality controls of SPOTS spleen data.

(a) Correlation of normalized ADT levels and mRNA expressions between two biological replicates of mouse spleen. The blue lines represent linear regression lines and 95% confident intervals are shown as gray shades. (b) Correlation between mRNA and different ADT levels (UMI) at single spatial barcode level for B cell, T cell, and macrophage enriched clusters across spatial barcodes in two biological replicates. The blue lines represent linear regression lines and 95% confident intervals are shown as gray shades. (c) Boxplot showing mRNA expression levels of germinal center (GC) specific genes (GSE12366; n = 163 genes) as a function of the distance from the center of GCs. The boxes were colored by the physical distance from the center of GCs as shown in Fig. 1f. Each boxplot ranges from the first and third quartiles with median shown as middle line, and the whiskers represents 1.5 times the interquartile range. (d) Cell-type deconvolution based on ADTs (Z-score) of each spatial barcode overlaid onto the spleen tissue. Magnified areas are shown in Fig. 1h.