Fig. 2: Spatial profiling of chromatin accessibility in FFPE mouse brains.
From: Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
a Spatial-FFPE-ATAC-seq on an FFPE mouse brain section (sample S4_2). Left: tissue scanning after microfluidic device barcoding. Middle: spatial distribution of unique fragments. Right: spatial pattern and UMAP of each cluster. b Spatial mapping of accessibility score of selected marker genes in different clusters for spatial FFPE-ATAC-seq (samples: S4_1 and S4_2) and fresh frozen spatial ATAC-seq (sample: FF_1). c Quantification of ATAC-seq peaks in genomic features extracted from cerebellar region, comparing FF and FFPE samples. (FF: n = 3; FFPE: n = 6; two-tailed Student’s t test). Data are presented as mean ± SD. d Comparison of ATAC-signals of selected genes between FFPE and FF cerebellar clusters. e Integration of scRNA-seq data17 with spatial-FFPE-ATAC-seq (sample S4_2). f Spatial mapping of selected cell types identified through label transfer. CNINH1: cerebellar inhibitory neuron 1; CBGRC: cerebellar granular cells; MOL1: Mature Oligodendrocyte 1; TEGLU7: telencephalon excitatory neurons 7. Scale bar: 500 μm. ns: not significant. Source data are provided as a Source Data file.
