A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells

Kevin Chen; Kivilcim Ozturk; Ted Liefeld; Michael Reich; Jill P. Mesirov; Hannah Carter; Stephanie I. Fraley

STAR Protocols (Jun 2021)

A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells

Kevin Chen,
Kivilcim Ozturk,
Ted Liefeld,
Michael Reich,
Jill P. Mesirov,
Hannah Carter,
Stephanie I. Fraley

Affiliations

Kevin Chen: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
Kivilcim Ozturk: Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
Ted Liefeld: Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA
Michael Reich: Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA
Jill P. Mesirov: Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
Hannah Carter: Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
Stephanie I. Fraley: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; Corresponding author

Journal volume & issue: Vol. 2, no. 2
p. 100561

Abstract

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Summary: Here, we describe a protocol combining functional metrics with genomic data to elucidate drivers of within-cell-type heterogeneity via the phenotype-to-genotype link. This technique involves using fluorescence tagging to label and isolate cells grown in 3D culture, enabling high-throughput enrichment of phenotypically defined cell subpopulations by fluorescence-activated cell sorting. We then perform a validated phenotypically supervised single-cell analysis pipeline to reveal unique functional cell states, including genes and pathways that contribute to cellular heterogeneity and were undetectable by unsupervised analysis.For complete details on the use and execution of this protocol, please refer to Chen et al. (2020).

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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