Extended Data Fig. 3: Quantification of DNA fragments per slide-DNA-seq array.
From: Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
a, Nuclear (left) and mitochondrial (center) DNA fragments per bead obtained for tissues used in this study. Right, mitochondrial fraction of fragments. 4x, protocol variant with 4x tagmentation. Black lines on violin plots indicate the mean. b, slide-DNA-seq of the mouse cerebellum experiment in Fig. 1. Beads are colored by the number of nuclear fragments (left), mitochondrial DNA fragments (center), and fraction of mitochondrial DNA fragments (right). c, Visualization of representative convex hulls for different spatial bin values of k for k-nearest neighbor smoothing. Beads are colored by raw counts, insets show convex hulls for k = 1, 10, 25, and 50, centered on salmon colored beads. Hulls are generally circular except at the edge of the array. d, Distribution of mean fragments per 1 Mb genomic bin for different spatial bin values of k. The median diameter of the smoothed features is indicated in parentheses. e, Comparison of nuclear fragments (left) and effective diameter (right) per bead for different spatial bin values of k. Scale bars, 500 μm.
