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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Mar 27, 2026

Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq

Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq

Published on: August 25, 2020

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

Holly N Kersey¹, Dominic J Acri¹, Luke C Dabin²

¹Medical Neurosciences Graduate Program, Indiana University School of Medicine, Indianapolis, IN, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA.

Cell Reports Methods

|March 24, 2026

Summary

This summary is machine-generated.

Choosing the right nuclei isolation method is crucial for high-quality single-nucleus RNA sequencing (snRNA-seq) data. Different techniques impact cell type representation and data purity, affecting biological interpretations.

Keywords:

CP: biotechnology CP: neuroscience ambient RNA contamination data quality nuclei isolation snRNA-seq

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Last Updated: Mar 27, 2026

Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq

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Published on: August 25, 2020

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Published on: October 12, 2018

Author Spotlight: Enhancing Drug Discovery - Development of Automated, Standardized Protocols for Nuclei Extraction from Frozen Tissues

Author Spotlight: Enhancing Drug Discovery - Development of Automated, Standardized Protocols for Nuclei Extraction from Frozen Tissues

Published on: July 28, 2023

Area of Science:

Neuroscience
Genomics
Molecular Biology

Background:

Single-nucleus RNA sequencing (snRNA-seq) is vital for analyzing complex tissues, especially frozen or difficult-to-isolate samples.
Existing snRNA-seq protocols lack systematic evaluations of nuclei isolation method impacts on data quality and reproducibility.

Purpose of the Study:

To compare the effects of three distinct nuclei isolation strategies on snRNA-seq data quality.
To assess the influence of isolation methods on nuclear integrity, cell type proportions, and RNA contamination.

Main Methods:

Comparison of three nuclei isolation methods: sucrose gradient centrifugation, spin column, and a machine-assisted platform.
Analysis of brain tissue using snRNA-seq to evaluate cell type diversity, transcriptional homogeneity, and marker preservation.
Assessment of contamination from ambient, mitochondrial, and ribosomal RNAs.

Main Results:

All methods identified diverse cell types, but protocol-dependent variations in cell type proportions and marker preservation were observed.
The machine-assisted method demonstrated superior overall data quality, with lower contamination levels.
Nuclei isolation methodology significantly impacts transcriptional homogeneity and biological interpretation.

Conclusions:

Nuclei isolation strategy is a critical variable in snRNA-seq experiments.
Method choice directly influences the accuracy of cell type identification and downstream biological insights.
Standardizing or carefully selecting isolation protocols is essential for robust and reproducible snRNA-seq studies.