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Inference and effects of barcode multiplets in droplet-based single-cell assays

View ORCID ProfileCaleb A. Lareau, View ORCID ProfileSai Ma, View ORCID ProfileFabiana M. Duarte, View ORCID ProfileJason D. Buenrostro
doi: https://doi.org/10.1101/824003
Caleb A. Lareau
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
3Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
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  • For correspondence: caleblareau@g.harvard.edu jason_buenrostro@harvard.edu
Sai Ma
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
4Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Fabiana M. Duarte
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Jason D. Buenrostro
1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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  • For correspondence: caleblareau@g.harvard.edu jason_buenrostro@harvard.edu
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Abstract

A widespread assumption for single-cell analyses specifies that one cell’s nucleic acids are predominantly captured by one oligonucleotide barcode. However, we show that ~13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call “barcode multiplets”. We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that ~4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that ~5-7% of beads may contain multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.

Footnotes

  • https://github.com/caleblareau/bap

  • https://github.com/caleblareau/barcode-multiplets

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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. All rights reserved. No reuse allowed without permission.
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Posted October 30, 2019.
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Inference and effects of barcode multiplets in droplet-based single-cell assays
Caleb A. Lareau, Sai Ma, Fabiana M. Duarte, Jason D. Buenrostro
bioRxiv 824003; doi: https://doi.org/10.1101/824003
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Inference and effects of barcode multiplets in droplet-based single-cell assays
Caleb A. Lareau, Sai Ma, Fabiana M. Duarte, Jason D. Buenrostro
bioRxiv 824003; doi: https://doi.org/10.1101/824003

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