Analyses of murine lymph node endothelial cell subsets using single-cell RNA sequencing and spectral flow cytometry

Lutz Menzel; Maria Zschummel; Armin Rehm

doi:10.1016/j.xpro.2022.101267

Analyses of murine lymph node endothelial cell subsets using single-cell RNA sequencing and spectral flow cytometry

STAR Protoc. 2022 Apr 6;3(2):101267. doi: 10.1016/j.xpro.2022.101267. eCollection 2022 Jun 17.

Authors

Lutz Menzel¹, Maria Zschummel², Armin Rehm¹

Affiliations

¹ Translational Tumorimmunology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.
² Microenvironmental Regulation in Autoimmunity and Cancer, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.

Abstract

Blood endothelial cells (BECs) in lymph nodes are distinct stromal cells with a transcriptional profile allowing fast and specific adaptation to the functional requirements. Here, we describe a step-by-step protocol for the enzymatic digestion of lymph nodes, the enrichment of stromal cells, the sorting of BECs, and the processing of BEC-related data for modern analysis approaches as spectral flow cytometry and single-cell RNA sequencing (scRNA-seq). For complete details on the use and execution of this protocol, please refer to Menzel et al. (2021).

Keywords: Bioinformatics; Cancer; Cell isolation; Flow Cytometry/Mass Cytometry; Genomics; Immunology; RNAseq; Single Cell.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Endothelial Cells*
Flow Cytometry / methods
Lymph Nodes / pathology
Mice
Sequence Analysis, RNA / methods
Single-Cell Analysis* / methods