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Targeting individual cells by barcode in pooled sequence libraries

Navpreet Ranu, Alexandra-Chloé Villani, Nir Hacohen, Paul C. Blainey
doi: https://doi.org/10.1101/178681
Navpreet Ranu
1Department of Biological Engineering, Massachusetts Institute of Technology, Massachusetts, USA
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Alexandra-Chloé Villani
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Nir Hacohen
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
3Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, Massachusetts, USA
4Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Paul C. Blainey
1Department of Biological Engineering, Massachusetts Institute of Technology, Massachusetts, USA
2Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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  • For correspondence: pblainey@broadinstitute.org
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Abstract

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 protocols1-5. However, researchers must sequence a large number of cells to sample rare subpopulations6-8, 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) subset7, 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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 20, 2017.
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Targeting individual cells by barcode in pooled sequence libraries
Navpreet Ranu, Alexandra-Chloé Villani, Nir Hacohen, Paul C. Blainey
bioRxiv 178681; doi: https://doi.org/10.1101/178681
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Targeting individual cells by barcode in pooled sequence libraries
Navpreet Ranu, Alexandra-Chloé Villani, Nir Hacohen, Paul C. Blainey
bioRxiv 178681; doi: https://doi.org/10.1101/178681

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