Fig. 1

Scifi-ATAC-seq combines pre-indexing with droplet-based scATAC-seq. a Schematic of regular droplet-based 10X Genomics scATAC-seq experimental workflow. b Schematic of scifi-ATAC-seq experimental workflow. c Distributions of the proportion of Tn5 integration sites within the promoter regions, encompassing the 2-kb flanking regions around gene transcription start sites (TSSs). d Distributions of the proportion of Tn5 integration sites within peaks per nucleus. e Distribution of unique Tn5 integration sites per nucleus. f Number of nuclei that passed quality control thresholds. g–i Scatterplot displaying the number of reads per cell classified as B73 or Mo17, color-coded by genotype classification. g 16 k input B73/Mo17 scATAC-seq; h 100 k scifi-ATAC-seq; i 200 k scifi-ATAC-seq. Median contamination rate: the median cross-contamination rate, attributed to index hopping, among all predicted singlets. j UMAP of all nuclei (n = 98,424). Nuclei are colored by their predicted cell type. k Pseudobulk cell type Tn5 integration site coverage around the phloem precursor marker ZmSMXL3. Vas. par. precursor: Vascular parenchyma precursor. l Pseudobulk cell type Tn5 integration site coverage for and UMAP embeddings overlaid with gene chromatin accessibility around the ZmSMXL3 gene across all datasets. N, number of phloem nuclei