Summary

Transcriptional profiling of thousands of single cells in parallel by RNA-seq is now routine. However, due to reliance on pooled library preparation, targeting analysis to particular cells of interest is difficult. Here, we present a multiplexed PCR method for targeted sequencing of select cells from pooled single-cell sequence libraries. We demonstrated this molecular enrichment method on multiple cell types within pooled single-cell RNA-seq libraries produced from primary human blood cells. We show how molecular enrichment can be combined with FACS to efficiently target ultra-rare cell types, such as the recently identified AXL+SIGLEC6+ dendritic cell (AS DC) subset, in order to reduce the required sequencing effort to profile single cells by 100-fold. Our results demonstrate that DNA barcodes identifying cells within pooled sequencing libraries can be used as targets to enrich for specific molecules of interest, for example reads from a set of target cells.

Overall design

10X libraries were prepared from two FACs sorted populations (HLA-DR and CD19) followed by enrichment for targeted single cells in triplicate. Enrichment was achieved with multiplex PCR with primers targeting the single cell barcodes that are added through library preparation.

Contributors

Navpreet Ranu 1, Alexandra-Chloé Villani 2 3 4, Nir Hacohen 2 3 4, Paul C Blainey 1 2

Contact

To be supplemented.