Extended Data Fig. 4: Clustering of spatial ATAC data with spatially aware factor analysis, marker genes and gene ontology analysis.
From: Solid-phase capture and profiling of open chromatin by spatial ATAC
a. Spatial ATAC clusters based on LSI (top; sections and clusters from Fig. 1c shown again for comparison) or NMF (bottom) for dimensionality reduction. b. Heatmap displaying the percentage of spots assigned to LSI- or NMF-computed clusters. c. Spatial activity plots for selected factors enriched in forebrain, facial prominence, liver, and limb. d. Examples of the most contributing peaks for each factor represented in c. Scale bars are 500 µm. e. Heatmap showing scaled accessibility for the top differentially accessible genes (gene body + promoter) across clusters. Relevant markers are highlighted. f. Gene ontology enrichment analysis of the top marker genes colored by cluster. P values were determined with hypergeometric test followed by correction for multiple testing using g:Profiler’s g:SCS algorithm.
