Protocol to dissociate, process, and analyze the human lung tissue using single-cell RNA-seq

STAR Protoc. 2022 Oct 21;3(4):101776. doi: 10.1016/j.xpro.2022.101776. eCollection 2022 Dec 16.

Abstract

We report a protocol for obtaining high-quality single-cell transcriptomics data from human lung biospecimens acquired from core needle biopsies, fine-needle aspirates, surgical resection, and pleural effusions. The protocol relies upon the brief mechanical and enzymatic disruption of tissue, enrichment of live cells by fluorescence-activated cell sorting (FACS), and droplet-based single-cell RNA sequencing (scRNA-seq). The protocol also details a procedure for analyzing the scRNA-seq data. For complete details on the use and execution of this protocol, please refer to Chan et al. (2021).

Keywords: Cancer; Cell isolation; Flow cytometry/Mass cytometry; Molecular biology; RNAseq; Sequence analysis; Sequencing; Single cell.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biopsy, Fine-Needle / methods
  • Gene Expression Profiling* / methods
  • Humans
  • Lung*
  • RNA-Seq
  • Sequence Analysis, RNA / methods