Integrated analysis of multimodal single-cell data

Cell, Journal Year: 2021, Volume and Issue: 184(13), P. 3573 - 3587.e29

Published: May 31, 2021

The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, unsupervised framework to learn the relative utility each data type in cell, enabling integrative analysis modalities. We apply our procedure a CITE-seq dataset 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending 228 antibodies construct reference atlas circulating immune system. Multimodal substantially improves ability resolve cell states, allowing us identify validate previously unreported lymphoid subpopulations. Moreover, demonstrate how leverage this rapidly map new datasets interpret responses vaccination coronavirus disease 2019 (COVID-19). Our approach broadly applicable strategy analyze look beyond transcriptome toward unified definition identity.

Language: Английский

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Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

Nature Methods, Journal Year: 2014, Volume and Issue: 11(4), P. 417 - 422

Published: March 2, 2014

Language: Английский

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viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

Nature Biotechnology, Journal Year: 2013, Volume and Issue: 31(6), P. 545 - 552

Published: May 19, 2013

Language: Английский

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Mass Cytometry: Single Cells, Many Features

Cell, Journal Year: 2016, Volume and Issue: 165(4), P. 780 - 791

Published: May 1, 2016

Language: Английский

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An Immune Atlas of Clear Cell Renal Cell Carcinoma

Cell, Journal Year: 2017, Volume and Issue: 169(4), P. 736 - 749.e18

Published: May 1, 2017

Language: Английский

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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

European Journal of Immunology, Journal Year: 2019, Volume and Issue: 49(10), P. 1457 - 1973

Published: Oct. 1, 2019

These guidelines are a consensus work of considerable number members the immunology and flow cytometry community. They provide theory key practical aspects enabling immunologists to avoid common errors that often undermine immunological data. Notably, there comprehensive sections all major immune cell types with helpful Tables detailing phenotypes in murine human cells. The latest techniques applications also described, featuring examples data can be generated and, importantly, how analysed. Furthermore, tips, tricks pitfalls avoid, written peer-reviewed by leading experts field, making this an essential research companion.

Language: Английский

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Normalization of mass cytometry data with bead standards

Cytometry Part A, Journal Year: 2013, Volume and Issue: 83A(5), P. 483 - 494

Published: March 19, 2013

Mass cytometry uses atomic mass spectrometry combined with isotopically pure reporter elements to currently measure as many 40 parameters per single cell. As any quantitative technology, there is a fundamental need for quality assurance and normalization protocols. In the case of cytometry, signal variation over time due changes in instrument performance intervals between scheduled maintenance must be accounted then normalized. Here, samples were mixed polystyrene beads embedded metal lanthanides, allowing monitoring multiple days data acquisition. The protocol described here includes simultaneous measurements cells on cytometer, subsequent extraction bead-based signature, application an algorithm enabling correction both short- long-term fluctuations. intensity that remains after may also used determine quality. Application one-month longitudinal analysis human peripheral blood sample reduced range median fluctuation from 4.9-fold 1.3-fold. © 2013 International Society Advancement Cytometry

Language: Английский

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Revealing the vectors of cellular identity with single-cell genomics

Nature Biotechnology, Journal Year: 2016, Volume and Issue: 34(11), P. 1145 - 1160

Published: Nov. 1, 2016

Language: Английский

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Human immune system variation

Nature reviews. Immunology, Journal Year: 2016, Volume and Issue: 17(1), P. 21 - 29

Published: Dec. 5, 2016

Language: Английский

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histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

Nature Methods, Journal Year: 2017, Volume and Issue: 14(9), P. 873 - 876

Published: Aug. 7, 2017

Language: Английский

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