Omics · study · 2026
Comparative analysis of nuclei isolation protocols for transcriptomic profiling of brain tissue
Listed in NCBI GEO
Single-nucleus RNA sequencing (snRNA-seq) enables gene expression analysis at the single-cell level in complex tissues like the brain.
Description
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.
Read the rest (1 more)
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.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE290nnn/GSE290858 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290858 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1230269 ncbi.nlm.nih.gov/bioproject/PRJNA1230269 ↗
project · from NCBI GEO
- PubMed 41875869 pubmed.ncbi.nlm.nih.gov/41875869 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Mus musculus
- From keywords
- Life Sciences
- Inferred from text
- Disease 75% · RNA sequencing 75% · Sequencing 75% · Single-cell RNA sequencing 65%
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE290858 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[disease].local:disease:disease | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:single-cell-rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[organism].NCBITaxon:10090 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |