February 5, 2015  |  Announcements, Publications, User Stories  |  By  |  0 Comments

New Breakthrough Method in Mass Cytometry

Zunder and Finck et al., from the Nolan Lab at Stanford University report new cell barcoding reagents for mass cytometry that incorporate the previously unused element palladium, expanding the number of mass cytometry measurement parameters by six. Leveraging this methodology, they present a new barcoding scheme which can be used to identify and remove cell doublets, as well as provide software that deconvolves barcoded datasets via a “single-cell debarcode” algorithm [1].

The dataset for this paper is hosted and publicly available on Cytobank Community; a free resource for the analysis, workflow, and protocols represented in this paper. Cytobank is the cloud-based analytics platform for single cell analysis. In Cytobank you can easily access and analyze multi-parameter data, visualize findings, produce high-impact graphics, and securely connect and collaborate with colleagues around the world.

About the authors:

Eli Zunder is a postdoc in Garry Nolan’s laboratory at Stanford University.  His research interests include mapping the transitions that occur during cellular reprogramming and differentiation, and identifying the molecular determinants of cell fate. He is also interested in developing new single-cell technologies to aid in these pursuits.
Q: How do you use Cytobank in your research?
A: I use Cytobank to store my FCS files, gate and analyze my data, and create figures for publication.  I use it a lot!
Rachel Finck is a Data Analyst in Garry Nolan’s laboratory at Stanford University, where she has developed computational methods for the processing, analysis and visualization of mass cytometry data. She is also interested in high-dimensional imaging and, more broadly, exploring data generated by new measurement technologies.
Q: How do you use Cytobank in your research?
A: I use Cytobank to store and share FCS files, and to gate and compare cell populations of interest. Right now I have three Cytobank tabs open in my browser!


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

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.

[1] Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Zunder E and Finck R et al. Nature Protocols (2015) 10, 316–333. doi:10.1038/nprot.2015.020