Single-cell RNA sequencing data for a mixed population of K562 cells and THP-1 cells, encoded with combinatorial DNA barcodes.

Microdroplet-based co-culturing assays dissect a complex multi-cellular interactions into individual cell-cell interaction events in a highly parallelized manner. To integrate single-cell sequencing approaches into such in-droplet multicellular co-culturing assays, we demonstrate a chemistry approach for encoding the identity of droplets to their belonging cells. K562 cells and THP-1 cells were encapsulated in water-in-oil droplets, where they were labeled with DNA barcodes encoding the identity of individual droplets. Then cells were released from droplets for pooled single-cell RNA sequencing. cDNA and DNA barcodes were sequenced in separate sequencing libraries. Experiments were carried out in duplicate.