CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics

High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-based multiplexing approach, CellTag Indexing, which uses predefined genetic barcodes that are also heritable, enabling cell populations to be tagged, pooled, and tracked over time in the same experimental replicate. We demonstrate the utility of CellTag Indexing by sequencing transcriptomes using a variety of cell types, including long-term tracking of cell engraftment and differentiation in vivo. Together, this presents CellTag Indexing as a broadly applicable genetic multiplexing tool that is complementary with existing single-cell technologies. Overall design: RNA sequencing of single transcriptomes and detection of sample identity by CellTag barcodes in 2-tag species mixing of MEF and HEK293T cells, 5-tag species mixing of MEF and HEK293T cells, and iEP-engrafted mouse colon.