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Comparative analysis of nuclei isolation protocols for transcriptomic profiling of brain tissue

ABSTRACT: Single-nucleus RNA sequencing (snRNA-seq) enables gene expression analysis at the single-cell level in complex tissues like the brain. The technique's effectiveness depends on obtaining high-quality nuclei suspensions, characterized by high yield, minimal cell-type biases, low contamination, and accurate gene expression profiles. This study compares three nuclei isolation methods using mouse brain tissue: sucrose gradient centrifugation, a spin column-based method, and a machine-assisted platform. Sucrose gradient centrifugation yielded the highest nuclei recovery with minimal doublets. The machine-assisted platform produced the highest viability with the lowest mitochondrial and RNA contamination. The column-based method had the lowest nuclei yield and highest ambient RNA contamination. These findings highlight the impact of isolation techniques on snRNA-seq data quality, with implications for optimizing neuroscience research and improving the study of brain cell-type diversity and disease mechanisms at the single-nucleus level.

ORGANISM(S): Mus musculus

PROVIDER: GSE290858 | GEO | 2026/03/05

REPOSITORIES: GEO

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