Indexing strategies for tagmentation-based single-cell assays. (A) Physical isolation of single cells into individual rection vessels that are then lysed and processed individually using the standard tagmentation workflows. Indexed PCR on each reaction compartment enables single-cell discrimination. (B) In situ tagmentation is performed by performing the tagmentation reaction in bulk to produce a single cell's library contained within the nucleus of that cell. These preprocessed nuclei can then be subjected to indexing via several techniques, including sorting and indexing PCR in plates (arrow 1), droplet encapsulation with indexing PCR or primer extension (arrow 2), or combinatorial indexing strategies using ligation (arrow 3). (C) Tagmentation with a large set of indexed adapters corresponding to individual reaction wells enables the IST nuclei to then be pooled and redistributed for a second round of indexing, enabling single-cell discrimination using the combination of indexes. The preindexed nuclei can also be carried through additional rounds of indexing using ligation-based methods (arrow 4) or droplet-based methods to enable increased throughput (arrow 5).
