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

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 organoidderived 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).

Automated summary

We present a protocol for single-cell RNA sequencing of SARS-CoV-2-infected human induced pluripotent stem cell (iPSC)-derived kidney organoids. The protocol involves obtaining single-cell suspensions through mechanical and enzymatic disruption of the organoids, followed by processing the cells into sequencing-ready SARS-CoV-2-targeted libraries. Sequencing analysis reveals alterations in kidney cells post virus infection.