Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm (original) (raw)

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Acknowledgements

We thank A. Trejo and A. Jager for mass cytometry quality control and instrument maintenance. We thank E. Simonds and P. Krutzik for their helpful discussions. This work was supported by grants from the US National Institutes of Health (NIH) (U19 AI057229, U54CA149145, N01-HV-00242, 1U19AI100627, 5R01AI07372405, R01CA184968, 1 R33 CA183654, NRSA F32 GM093508-01, 152175.5041015.0412 and R01 A1073724), NIH-the Baylor Research Institute (41000411217), the NIH-Northrop Grumman Corp. (7500108142), the California Institute for Regenerative Medicine (CIRM) (DR1-01477, RB2–01592), the US Department of Defense (OC110674), the European Commission (Health.2010.1.2-1), the US Food and Drug Administration (HHSF223201210194C), the Bill and Melinda Gates Foundation (OPP 1017093), the Alliance for Lupus Research, the Lymphoma Research Foundation, the Entertainment Industry Foundation (National Women's Cancer Research Alliance grant) and the National Science Foundation CAREER award (MCB-1149728). D.P. holds a Packard Fellowship for Science and Engineering. G.P.N. holds the Rachford and Carlota A. Harris Endowed Professorship.

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Author notes

  1. Bernd Bodenmiller
    Present address: Present address: Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.,
  2. Eli R Zunder and Rachel Finck: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Microbiology and Immunology, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, California, USA
    Eli R Zunder, Rachel Finck, Gregory K Behbehani, Veronica D Gonzalez, Cynthia G Lorang, Zach Bjornson, Matthew H Spitzer, Bernd Bodenmiller, Wendy J Fantl & Garry P Nolan
  2. Divisions of Hematology and Oncology, Stanford University School of Medicine, Stanford, California, USA
    Gregory K Behbehani
  3. Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York, USA
    El-ad D Amir, Smita Krishnaswamy & Dana Pe'er

Authors

  1. Eli R Zunder
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  2. Rachel Finck
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  3. Gregory K Behbehani
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  4. El-ad D Amir
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  5. Smita Krishnaswamy
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  6. Veronica D Gonzalez
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  7. Cynthia G Lorang
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  8. Zach Bjornson
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  9. Matthew H Spitzer
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  10. Bernd Bodenmiller
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  11. Wendy J Fantl
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  12. Dana Pe'er
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  13. Garry P Nolan
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Contributions

E.R.Z. developed the palladium MCB reagents and labeling protocol, implemented the doublet-filtering barcode scheme, developed the single-cell debarcoding algorithm, designed and performed the experiments, analyzed the data and wrote the manuscript; R.F. developed the single-cell debarcoding algorithm, designed and implemented the debarcoding software, designed the experiments, analyzed the data and wrote the manuscript; G.K.B. developed the palladium MCB reagents and labeling protocol, developed the saponin-mediated MCB labeling and wrote the manuscript; E.D.A. developed the doublet-filtering barcode scheme; S.K. assisted with developing barcode deconvolution methods; V.D.G. performed experiments; C.G.L. performed experiments; Z.B. performed experiments and wrote the manuscript; M.H.S. performed experiments; B.B. developed the palladium MCB reagents and labeling protocol; W.J.F. designed the experiments and wrote the manuscript; D.P. developed the doublet-filtering barcode scheme and wrote the manuscript; G.P.N. designed the experiments and wrote the manuscript.

Corresponding author

Correspondence toGarry P Nolan.

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Competing interests

G.P.N. has a personal financial interest in the company Fluidigm, the manufacturer of the mass cytometer used in this manuscript. R.F. has been a paid consultant for the company DVS Sciences, the original manufacturer of the mass cytometer that has since merged with Fluidigm. G.K.B. has been a paid consultant for both DVS Sciences and Fluidigm.

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Zunder, E., Finck, R., Behbehani, G. et al. Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.Nat Protoc 10, 316–333 (2015). https://doi.org/10.1038/nprot.2015.020

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