title: sci-ATAC-seq of Arabidopsis root
design: To demonstrate the utility of sci-ATAC-seq to resolve heterogeneous chromatin accessibility signals from complex plant tissues, we applied it to whole root tissues from 2-week-old A. thaliana plants. First, fixed nuclei were molecularly tagged in four 96-well plates with 24x16 barcoded TS-Tn5 transposase complexes to integrate 384 diverse sequencing adapters into ACRs of individual nuclei. The tagmentation reaction is then quenched, the tagged nuclei are pooled and redistributed to multiple 96-wells plates with approximately 15 nuclei per well. Plate PCR was then performed using 12x8 sets of unique dual-indexed primers complementary to the transposase-introduced adapters, which added the second round well-specific barcode to the Tn5-tagged DNA. Subsequently, PCR products from individual wells in each plate are combined and purified, and a final round of PCR is performed to add a third barcode into each molecule to index the sample plate. In this method, a single 96-well plate could generate sci-ATAC-seq profiles for ~1,500 cells, and one could easily perform 10-20 plate PCR to obtain 15,000-30,000 epigenome profiles, making this method highly scalable.