Fig. 2

Multiplexing eight samples with scifi-ATAC-seq. a Well assignment showing the multiplexing of primary samples and genotypes. b Number of profiled nuclei for each genotype. Est. Collision: estimated cell barcode collisions within the same genotype. c Spearman correlation heatmap among the 8 libraries(SS, stiff stalk; NSS, non-stiff stalk; TS, tropical/subtropical; Mixed, mixed tropical-temperate). d UMAP of all nuclei (n = 124,656). Nuclei are colored by their predicted cell type. Vas. par. precursor: vascular parenchyma precursor, procambium phloem pre.: procambium phloem precursor. e UMAP of all nuclei across the eight samples. f Chromatin accessibility of cell-type-specific accessible chromatin regions (ctACRs, Z-score > 2) among all cell types. g Pseudobulk cell type Tn5 integration site coverage around the phloem precursor marker ZmSMXL3. h Pseudobulk cell type Tn5 integration site coverage and UMAP embeddings overlaid with gene chromatin accessibility around the ZmSMXL3. N, nuclei number of procambium phloem precursor. i Chromatin accessibility of genotype-specific accessible chromatin regions (gtACRs) among seven genotypes. The number of gtACRs was labeled. j Pseudobulk cell type Tn5 integration site coverage with gene chromatin accessibility around the Zm00001eb280310 across all samples in procambium phloem precursor cells