Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing.

ABSTRACT: Single-nucleus RNA sequencing (snRNA-seq) enables resolving cellular heterogeneity in complex tissues. snRNA-seq overcomes limitations of traditional single-cell RNA-seq by using nuclei instead of cells, allowing to utilize frozen tissues and difficult-to-isolate cell types. Although various nuclei isolation methods have been developed, systematic evaluations of their effects on nuclear integrity and subsequent data quality remain lacking, a critical gap with profound implications for the rigor and reproducibility. To address this, we compared three mechanistically distinct nuclei isolation strategies with brain tissues: a sucrose gradient centrifugation-based method, a spin column-based method, and a machine-assisted platform. All methods successfully captured diverse cell types but revea

SUBMITTER: Kersey HN 

PROVIDER: S-EPMC11974938 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature