Extended Data Fig. 8 |. Quality control metrics for spatial-Mux-seq datasets.

Sample: 5M_20_μm. a, Spatial-Mux-seq profiling of ATAC, H3K27me3, H3K27ac, RNA, and proteins from EAE mouse brain section. Left: tissue scanning of the region of interest, aligned with the region annotation of a corresponding section from Allen Mouse Brain Atlas (P56). Middle and right: 20-μm-microfluidic device with 100×100 pixels. Two-time spatial barcodes (A_1–100 and B_1–100) were sequentially flowed over tissue section. The red square highlights the region captured for spatial analysis. b, Unique fragments, gene feature counts, and protein counts in spatial-Mux-seq mapping of five months mouse brain obtained with 20-μm pixel size. c, Scatterplots showing the TSS enrichment score vs unique nuclear fragments per pixel for three modalities: ATAC, H3K27me3 and H3K27ac. d, Violin plots of unique fragments and TSS enrichment values of ATAC, H3K27ac, and H3K27me3. e, Violin plots of gene counts and gene UMIs distribution. f, Violin plots of protein counts and protein UMIs distribution. d-f, Number of pixels in 5M_20_μm, 9,688. Box plots show the median (center line), the first and third quartiles (box limits) and 1.5x interquartile range (whiskers). Scale bar: 500 μm.