Protocol to identify and isolate rare murine tumor-resident dendritic cell populations for low-input transcriptomic profiling

Athanasios Papadas; Daniel J. Lagal; Yaling Dou; Duncan Hong; Alicia Gibbons; Alexander Cicala; Yun Huang; Brolyn Zomalan; Elsa Molina; Fotis Asimakopoulos

STAR Protocols (Sep 2024)

Protocol to identify and isolate rare murine tumor-resident dendritic cell populations for low-input transcriptomic profiling

Athanasios Papadas,
Daniel J. Lagal,
Yaling Dou,
Duncan Hong,
Alicia Gibbons,
Alexander Cicala,
Yun Huang,
Brolyn Zomalan,
Elsa Molina,
Fotis Asimakopoulos

Affiliations

Athanasios Papadas: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA; Corresponding author
Daniel J. Lagal: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
Yaling Dou: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
Duncan Hong: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
Alicia Gibbons: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
Alexander Cicala: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
Yun Huang: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
Brolyn Zomalan: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
Elsa Molina: Next Generation Sequencing Core, The Salk Institute for Biological Studies, La Jolla, CA, USA
Fotis Asimakopoulos: Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA; Corresponding author

Journal volume & issue: Vol. 5, no. 3
p. 103195

Abstract

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Summary: Conventional type 1 dendritic cells (cDC1s) are critical for innate sensing of cancer, yet they are scarce in the tumor microenvironment (TME). Here, we present a protocol to identify and isolate cDC1 subsets from murine implantable tumors for subsequent transcriptomic profiling using a flow sorting-based strategy. We describe steps for cell culture of mouse tumors, tumoral growth, dissociation and isolation of tumoral cells, extracellular staining, and cell sorting. We then detail procedures for RNA isolation, mRNA library preparation, and sequencing.For complete details on the use and execution of this protocol, please refer to Papadas et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

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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