Targeting individual cells by barcode in pooled sequence libraries
Author(s)Villani, Alexandra-Chloé; Blainey, Paul C; Ranu, Navpreet Singh; Hacohen, Nir
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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.
DepartmentMassachusetts Institute of Technology. Department of Biological Engineering
Nucleic Acids Research
Oxford University Press
Ranu, Navpreet, Alexandra-Chloé Villani, Nir Hacohen, and Paul C Blainey. “Targeting Individual Cells by Barcode in Pooled Sequence Libraries.” Nucleic Acids Research 47, no. 1 (September 26, 2018): e4–e4.
Final published version