Normalization of mass cytometry data with bead standards
Rachel Finck,Erin F. Simonds,Astraea Jager,Smita Krishnaswamy,Karen Sachs,Wendy J. Fantl,Dana Pe'er,Garry P. Nolan,Sean C. Bendall +8 more
TLDR
The protocol described here includes simultaneous measurements of beads and cells on the mass cytometer, subsequent extraction of the bead‐based signature, and the application of an algorithm enabling correction of both short‐ and long‐term signal fluctuations.Abstract:
Mass cytometry uses atomic mass spectrometry combined with isotopically pure reporter elements to currently measure as many as 40 parameters per single cell. As with any quantitative technology, there is a fundamental need for quality assurance and normalization protocols. In the case of mass cytometry, the signal variation over time due to changes in instrument performance combined with intervals between scheduled maintenance must be accounted for and then normalized. Here, samples were mixed with polystyrene beads embedded with metal lanthanides, allowing monitoring of mass cytometry instrument performance over multiple days of data acquisition. The protocol described here includes simultaneous measurements of beads and cells on the mass cytometer, subsequent extraction of the bead-based signature, and the application of an algorithm enabling correction of both short- and long-term signal fluctuations. The variation in the intensity of the beads that remains after normalization may also be used to determine data quality. Application of the algorithm to a one-month longitudinal analysis of a human peripheral blood sample reduced the range of median signal fluctuation from 4.9-fold to 1.3-fold.read more
Citations
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Integrated analysis of multimodal single-cell data
Yuhan Hao,Stephanie Hao,Erica Andersen-Nissen,William M. Mauck,Shiwei Zheng,Andrew Butler,Maddie Jane Lee,Aaron J. Wilk,Charlotte A. Darby,Michael Zager,Paul Hoffman,Marlon Stoeckius,Efthymia Papalexi,Eleni P. Mimitou,Jaison Jain,Avi Srivastava,Tim Stuart,Lamar M. Fleming,Bertrand Z. Yeung,Angela J. Rogers,Juliana M. McElrath,Catherine A. Blish,Raphael Gottardo,Peter Smibert,Rahul Satija +24 more
TL;DR: Weighted-nearest neighbor analysis as mentioned in this paper is an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities.
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Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
Jacob H. Levine,Erin F. Simonds,Sean C. Bendall,Kara L. Davis,El-ad David Amir,Michelle D. Tadmor,Oren Litvin,Harris G. Fienberg,Astraea Jager,Eli R. Zunder,Rachel Finck,Amanda Larson Gedman,Ina Radtke,James R. Downing,Dana Pe'er,Garry P. Nolan +15 more
TL;DR: Using hematopoietic progenitors, a signaling-based measure of cellular phenotype was defined, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts, yielding insights into AML pathophysiology.
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Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment.
Elham Azizi,Ambrose J. Carr,Ambrose J. Carr,George Plitas,Andrew E. Cornish,Catherine Konopacki,Sandhya Prabhakaran,Juozas Nainys,Juozas Nainys,Kenmin Wu,Vaidotas Kiseliovas,Vaidotas Kiseliovas,Manu Setty,Kristy Choi,Rachel M. Fromme,Phuong Dao,Peter T. McKenney,Peter T. McKenney,Ruby C. Wasti,Krishna Kadaveru,Linas Mazutis,Alexander Y. Rudensky,Dana Pe'er +22 more
TL;DR: A preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, are developed to address computational challenges inherent to single-cell data and support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer.
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Mass Cytometry: Single Cells, Many Features.
TL;DR: The current state of mass cytometry is reviewed, providing an overview of the instrumentation, its present capabilities, and methods of data analysis, as well as thoughts on future developments and applications.
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Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development
Sean C. Bendall,Kara L. Davis,El-ad David Amir,Michelle D. Tadmor,Erin F. Simonds,Tiffany J. Chen,Daniel K. Shenfeld,Garry P. Nolan,Dana Pe'er +8 more
TL;DR: This study provides a comprehensive analysis of human B lymphopoiesis, laying a foundation to apply this approach to other tissues and "corrupted" developmental processes including cancer.
References
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Journal ArticleDOI
Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators
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Journal ArticleDOI
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Journal ArticleDOI
Quality assurance for polychromatic flow cytometry
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