Benchmarking of Single Nuclei Rna-Seq Methods on Human Post-Mortem Brain Tissue

Abstract

Molecular analysis of human post-mortem brain tissue by single nuclei RNA-sequencing (snRNA-seq) holds the promise to identify disease associated mechanisms. In the fast-developing field of post-mortem snRNA-seq, the sample sizes of case/control studies have drastically increased over the last years. Still, to overcome the inter-individual genetic variability of psychiatric disorders, even larger cohorts are required. Benchmarking available methods is thus crucial for scaling studies in molecular psychiatry. We compared five commercially available methods using fresh frozen post-mortem human forebrain tissue samples. Using tissue samples from the same three donors for all methods, our investigation revealed comparable overall performance among the five methods. Our study suggests that the selection of snRNA-seq method should mainly be informed by the need of specific data and practical experimental considerations such as hardware requirements, ability to multiplex, tissue quantity input requirements, and transportation of samples/tissues.

Note:
Funding declaration: JHL was supported by the Swedish Research Council (VR) Dnr: 2024-03567), Swedish Brain Foundation (Hjärnfonden, award FO2024-0144-HK-49) and European Union (ERC grant 819540).

Conflict of Interests: The authors declare they have no competing interests.

Ethical Approval: The experiments were performed under ethical approval 2016/589-13 from the Swedish internal review board (Etikprövningsnämnden).

Keywords: Single nuclei RNA-sequencing, Benchmarking, Human post-mortem brain tissue