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Targeting individual cells by barcode in pooled sequence libraries

By Navpreet Ranu, Alexandra-ChloƩ Villani, Nir Hacohen, Paul C. Blainey

Posted 20 Aug 2017
bioRxiv DOI: 10.1101/178681 (published DOI: 10.1093/nar/gky856)

There is rising interest in applying single-cell transcriptome analysis and other single-cell sequencing methods to resolve differences between cells. Pooled processing of thousands of single cells is now routinely practiced by introducing cell-specific DNA barcodes early in cell processing protocols. However, researchers must sequence a large number of cells to sample rare subpopulations, even when fluorescence-activated cell sorting (FACS) is used to pre-enrich rare cell populations. Here, a new molecular enrichment method is used in conjunction with FACS enrichment to enable efficient sampling of rare dendritic cell (DC) populations, including the recently identified AXL+SIGLEC6+ (AS DCs) subset, within a 10X Genomics single-cell RNA-Seq library. DC populations collectively represent 1-2% of total peripheral blood mononuclear cells (PBMC), with AS DC representing only 1-3% of human blood DCs and 0.01-0.06% of total PBMCs.

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