GEO series

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

GSE290858 Mus musculus Expression profiling by high throughput sequencing 6 samples Submitted 2026/03/05 Platform GPL24247

Summary

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.

Published in

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

Kersey HN, Acri DJ, Dabin LC et al. · Cell reports methods 2026 · PMID 41875869 · doi:10.1016/j.crmeth.2026.101337

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Direct links to NCBI, no account and no request form: the whole study as GSE290858_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1230269 and SRA study SRP567179. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41875869) ↗

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