Targeting individual cells by barcode in pooled sequence libraries

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[1][1]-[5][2]. However, researchers must sequence a large number of cells to sample rare subpopulations[6][3]-[8][4], 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[7][5], 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. [1]: #ref-1 [2]: #ref-5 [3]: #ref-6 [4]: #ref-8 [5]: #ref-7