PMID- 32620586 OWN - NLM STAT- MEDLINE VI - 29 IP - 156 TI - Breathing fresh air into respiratory research with single-cell RNA sequencing. CI - Copyright ©ERS 2020. LA - eng PT - Journal Article PT - Review PL - England TA - Eur Respir Rev JT - European respiratory review : an official journal of the European Respiratory Society JID - 9111391 IS - 1600-0617 (Electronic) LID - 200060 [pii] LID - 10.1183/16000617.0060-2020 [doi] FAU - Alexander, Michael J AU - Alexander MJ AD - Northwestern University, Feinberg School of Medicine, Dept of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, USA. FAU - Budinger, G R Scott AU - Budinger GRS AD - Northwestern University, Feinberg School of Medicine, Dept of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, USA. FAU - Reyfman, Paul A AU - Reyfman PA AUID- ORCID: https://orcid.org/0000-0002-6435-6001 AD - Northwestern University, Feinberg School of Medicine, Dept of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, USA. IS - 0905-9180 (Linking) SB - IM MH - Computational Biology/methods MH - Gene Expression Profiling MH - Humans MH - Lung Diseases/*genetics MH - Pulmonary Medicine/*trends MH - Sequence Analysis, RNA/*methods MH - Single-Cell Analysis/*methods MH - Transcriptome PMC - PMC7719403 DCOM- 20210517 LR - 20221116 DP - 2020 Jun 30 DEP - 20200703 AB - The complex cellular heterogeneity of the lung poses a unique challenge to researchers in the field. While the use of bulk RNA sequencing has become a ubiquitous technology in systems biology, the technique necessarily averages out individual contributions to the overall transcriptional landscape of a tissue. Single-cell RNA sequencing (scRNA-seq) provides a robust, unbiased survey of the transcriptome comparable to bulk RNA sequencing while preserving information on cellular heterogeneity. In just a few years since this technology was developed, scRNA-seq has already been adopted widely in respiratory research and has contributed to impressive advancements such as the discoveries of the pulmonary ionocyte and of a profibrotic macrophage population in pulmonary fibrosis. In this review, we discuss general technical considerations when considering the use of scRNA-seq and examine how leading investigators have applied the technology to gain novel insights into respiratory biology, from development to disease. In addition, we discuss the evolution of single-cell technologies with a focus on spatial and multi-omics approaches that promise to drive continued innovation in respiratory research.