Frontiers in Cell and Developmental Biology (Apr 2022)

An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies

  • Blaž Burja,
  • Blaž Burja,
  • Blaž Burja,
  • Dominique Paul,
  • Aizhan Tastanova,
  • Sam G. Edalat,
  • Reto Gerber,
  • Reto Gerber,
  • Miranda Houtman,
  • Muriel Elhai,
  • Kristina Bürki,
  • Ramon Staeger,
  • Gaetana Restivo,
  • Ramon Lang,
  • Snezna Sodin-Semrl,
  • Katja Lakota,
  • Matija Tomšič,
  • Matija Tomšič,
  • Mitchell P. Levesque,
  • Oliver Distler,
  • Žiga Rotar,
  • Žiga Rotar,
  • Mark D. Robinson,
  • Mojca Frank-Bertoncelj,
  • Mojca Frank-Bertoncelj

DOI
https://doi.org/10.3389/fcell.2022.872688
Journal volume & issue
Vol. 10

Abstract

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We present an optimized dissociation protocol for preparing high-quality skin cell suspensions for in-depth single-cell RNA-sequencing (scRNA-seq) analysis of fresh and cultured human skin. Our protocol enabled the isolation of a consistently high number of highly viable skin cells from small freshly dissociated punch skin biopsies, which we use for scRNA-seq studies. We recapitulated not only the main cell populations of existing single-cell skin atlases, but also identified rare cell populations, such as mast cells. Furthermore, we effectively isolated highly viable single cells from ex vivo cultured skin biopsy fragments and generated a global single-cell map of the explanted human skin. The quality metrics of the generated scRNA-seq datasets were comparable between freshly dissociated and cultured skin. Overall, by enabling efficient cell isolation and comprehensive cell mapping, our skin dissociation-scRNA-seq workflow can greatly facilitate scRNA-seq discoveries across diverse human skin pathologies and ex vivo skin explant experimentations.

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