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

Nature Protocols volume 10, pages 316–333 (2015)Cite this article

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Abstract

Mass-tag cell barcoding (MCB) labels individual cell samples with unique combinatorial barcodes, after which they are pooled for processing and measurement as a single multiplexed sample. The MCB method eliminates variability between samples in antibody staining and instrument sensitivity, reduces antibody consumption and shortens instrument measurement time. Here we present an optimized MCB protocol. The use of palladium-based labeling reagents expands the number of measurement channels available for mass cytometry and reduces interference with lanthanide-based antibody measurement. An error-detecting combinatorial barcoding scheme allows cell doublets to be identified and removed from the analysis. A debarcoding algorithm that is single cell–based rather than population-based improves the accuracy and efficiency of sample deconvolution. This debarcoding algorithm has been packaged into software that allows rapid and unbiased sample deconvolution. The MCB procedure takes 3–4 h, not including sample acquisition time of ∼1 h per million cells.

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Figure 1: Isothiocyanobenzyl-EDTA(palladium) MCB cell labeling reagent.
Figure 2: MCB cell labeling by the isothiocyanobenzyl-EDTA(palladium) chelate.
Figure 3: Doublet-filtering MCB scheme.
Figure 4: Single-cell barcode deconvolution.
Figure 5: Single-cell debarcoding software.
Figure 6: Doublet removal with the 6-choose-3 MCB scheme and single-cell debarcoding.
Figure 7: Single-cell deconvolution versus Boolean gating for MCB samples with and without large differences in MCB labeling intensity.

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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

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  1. Eli R Zunder
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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 to Garry 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.

Integrated supplementary information

Supplementary Figure 1 Palladium barcode staining intensity across cell lines of different cell sizes.

BC2 (Pd104) staining intensity in surface marker gated OVCAR and U937 cells from five barcoded samples, all of which are positive for BC2. Debarcoding was done independently of cell type gating.

Supplementary Figure 2 Time-of-flight traces of palladium barcodes of singlets and doublets with overlapping event lengths and Ir-intercalator intensities.

(a) Example cell events are indicated on the event length x Ir-Intercalator biaxial plot. Event 1 is identified as a barcode singlet, but is of similar length and Ir-intercalator intensity as event 4, which has been identified as a barcode doublet. Similarly, event 2 is of similar length and Ir-Intercalator intensity as event 3. (b) The per-spectrum traces of the barcoding channels from the IMD files confirm the barcode and single/doublet assignments.

Supplementary Figure 3 Gates used for Figure 6b.

(a) Singlet gates of increasing stringency and their percent yields. (b) The percent of CD4+CD8+ cells within each of the singlet gates shown in (a).

Supplementary Figure 4 96-well plate layout for MCB reagent titration in triplicate.

(a) Serial dilution layout for the 6 Palladium MCB reagents. (b) Wells to pool before for mass cytometry measurement.

Supplementary Figure 5 Plate layout for 6-choose-3 MCB combinatorial doublet-filtering scheme.

(a) MCB reagent combinations to use for a 20 sample 6-choose-3 combinatorial doublet-filtering scheme. (b) Mapping the 20 samples to a 5 x 4 grid. (c) Pipetting guide for each of the 6 Palladium MCB reagents into the 5 x 4 grid.

Supplementary Figure 6 Pooled sample groups for 20-sample MCB combinatorial plate testing and validation.

Wells to pool for 8 pooled sample groups that will be used to validate the sample assignment and correct orientation of the tested 100X MCB combinatorial plate.

Supplementary information

Supplementary Text and Figures

Supplementary figures 1–6 (PDF 2386 kb)

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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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