Isolation of macrophages from mouse skin wounds for single-cell RNA sequencing

Research output: Contribution to journalResearch articleContributedpeer-review



Understanding macrophage heterogeneity in tissue repair is a major challenge. Here, we describe a protocol that combines isolation of immune cells from skin wounds with subsequent flow-cytometry-based sorting of wound macrophages and single-cell RNA sequencing. We use a modified version of the original Smart-seq2 protocol to increase speed and accuracy. This protocol is useful for analyzing the pronounced heterogeneity of activation phenotypes in wound macrophages and might be adapted to other experimental models of skin inflammation. For complete details on the use and execution of this protocol, please refer to Willenborg et al. (2021).


Original languageEnglish
Article number101337
JournalSTAR Protocols
Issue number2
Publication statusPublished - 19 Apr 2022

External IDs

PubMed 35496783
ORCID /0000-0003-1494-1162/work/142255069


DFG Classification of Subject Areas according to Review Boards

Subject groups, research areas, subject areas according to Destatis


  • Cell Biology, Cell isolation, Flow Cytometry/Mass Cytometry, Immunology, Metabolism, Molecular Biology, RNAseq, Sequencing, Single Cell, Wound Healing, Macrophages, Animals, Flow Cytometry, Sequence Analysis, RNA, Leukocyte Count, Mice