Targeting individual cells by barcode in pooled sequence libraries
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gky856.pdf
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Author(s)
Villani, Alexandra-Chloé
Blainey, Paul C
Ranu, Navpreet Singh
Hacohen, Nir
Date Issued
September 2018
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
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.
Version
Final published version
Abstract
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.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1093/nar/gky856
