Fig. 4: Spatial profiling of chromatin accessibility in FFPE human thymus.
From: Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
a Schematic illustration of experimental design: 50-μm ATAC (n = 2), 10-μm ATAC (n = 1), and H&E-staining (n = 1). b H&E-stained image of an adjacent tissue section. Dashed circle indicated overlapping area of spatial FFPE-ATAC-seq. Arrows labeled the cortex, septum, medulla, and medulla-cortex (MC) boundary. c, d Spatial FFPE-ATAC-seq profiling of FFPE human thymus sections with different resolutions. Left: tissue scanning before microfluidic device barcoding. Middle: spatial distribution of unique fragments. Right: spatial pattern and UMAP of each cluster. e Integration of scRNA-seq data20 with spatial-FFPE-ATAC-seq with different resolutions. f Spatial mapping of selected cell types identified through label transfer. TECs: medullary thymic epithelial cells. g, Spatial mapping of gene scores for selected marker genes in different clusters. h–m, 50-μm ATAC (h, j, l) and 10-μm ATAC(i, k, m) data were used for genome track (h, i) and pseudotime analysis (j–m). h–i Genome track visualization of selected marker genes across different clusters. j, k Pseudotemporal reconstruction of T cell development from cortex to medulla region. l, m, Dynamics of gene scores of CD8A and KRT5 along the pseudotime shown in (j, k) respectively. Scale bar: 500 μm.
