title: Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.
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.
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Eli R
authors.initials: ER
authors.lastname: Zunder
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Finck
authors.affiliation: 1] Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA. [2] Divisions of Hematology and Oncology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Gregory K
authors.initials: GK
authors.lastname: Behbehani
authors.affiliation: Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York, USA.
authors.forename: El-Ad D
authors.initials: el-AD
authors.lastname: Amir
authors.affiliation: Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York, USA.
authors.forename: Smita
authors.initials: S
authors.lastname: Krishnaswamy
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Veronica D
authors.initials: VD
authors.lastname: Gonzalez
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Cynthia G
authors.initials: CG
authors.lastname: Lorang
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Zach
authors.initials: Z
authors.lastname: Bjornson
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Matthew H
authors.initials: MH
authors.lastname: Spitzer
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Bernd
authors.initials: B
authors.lastname: Bodenmiller
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Wendy J
authors.initials: WJ
authors.lastname: Fantl
authors.affiliation: Department of Biological Sciences, Department of Systems Biology, Columbia University, New York, New York, USA.
authors.forename: Dana
authors.initials: D
authors.lastname: Pe'er
authors.affiliation: Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA.
authors.forename: Garry P
authors.initials: GP
authors.lastname: Nolan
mesh_terms: D000465:Algorithms; D005434:Flow Cytometry / Q000379:methods*; D010165:Palladium; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software; D013194:Staining and Labeling / Q000379:methods
chemical_list: D010165:Palladium