Using human iPSC-derived kidney organoids to decipher SARS-CoV-2 pathology on single cell level

STAR Protoc. 2022 Jul 19;3(3):101612. doi: 10.1016/j.xpro.2022.101612. eCollection 2022 Sep 16.


We describe a protocol for single-cell RNA sequencing of SARS-CoV-2-infected human induced pluripotent stem cell (iPSC)-derived kidney organoids. After inoculation of kidney organoids with virus, we use mechanical and enzymatic disruption to obtain single cell suspensions. Next, we process the organoid-derived cells into sequencing-ready SARS-CoV-2-targeted libraries. Subsequent sequencing analysis reveals changes in kidney cells after virus infection. The protocol was designed for kidney organoids cultured in a 6-well transwell format but can be adapted to organoids with different organ backgrounds. For complete details on the use and execution of this protocol, please refer to Jansen et al. (2022).

Keywords: Cell biology; Microbiology; Organoids; Single cell; Stem cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19*
  • Humans
  • Induced Pluripotent Stem Cells*
  • Kidney
  • Organoids
  • SARS-CoV-2