Extended Data Fig. 9: Spatial ATAC on human HER2-positive breast cancer.
From: Solid-phase capture and profiling of open chromatin by spatial ATAC
a. On the left, violin plot showing unique fragments per spot and percentage TSS fragments in three adjacent sections processed using spatial ATAC. On the right, TSS enrichment and insert size distribution. b. Spatial ATAC clustering reveals tumor, immune-rich and normal tissue regions. c. Cluster percentage across sections. d-e. UMAP embedding on spatial ATAC peaks color-coded by cluster or tissue section. f. Genome tracks showing normalized spatial ATAC-seq fragment density around the HER2 (ERBB2) locus colored by cluster. The gray area marks a previously described gene body enhancer36 shown in Fig. 2l. Scale bars are 500 µm.
