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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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Updated: Mar 28, 2026

Preparation of Cytoplasmic and Nuclear Long RNAs from Primary and Cultured Cells

Preparation of Cytoplasmic and Nuclear Long RNAs from Primary and Cultured Cells

Published on: April 7, 2023

Nuclear RNA Isolation and Sequencing.

Navroop K Dhaliwal¹, Jennifer A Mitchell²

¹Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, Canada, M5S 3G5.

Methods in Molecular Biology (Clifton, N.J.)

|January 2, 2016

Summary

This summary is machine-generated.

Nuclear-RNA sequencing (nucRNA-seq) captures both spliced and unspliced transcripts, including long noncoding RNAs. This method provides a more comprehensive view of the transcriptome than poly (A) RNA sequencing.

Keywords:

Cellular fractionation LncRNA Massively parallel sequencing Nuclear RNA Transcriptome profiling

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Last Updated: Mar 28, 2026

Preparation of Cytoplasmic and Nuclear Long RNAs from Primary and Cultured Cells

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Nuclei Isolation from Whole Tissue using a Detergent and Enzyme-Free Method

Nuclei Isolation from Whole Tissue using a Detergent and Enzyme-Free Method

Published on: June 24, 2020

Area of Science:

Genomics
Molecular Biology
Transcriptomics

Background:

Traditional transcriptome studies often rely on polyadenylated (poly (A)) RNA sequencing.
Poly (A) RNA sequencing primarily reflects steady-state messenger RNA (mRNA) levels.
This approach may not accurately represent transcriptional regulation and can miss non-polyadenylated transcripts like long noncoding RNAs.

Purpose of the Study:

To introduce nuclear-RNA sequencing (nucRNA-seq) as a method to comprehensively analyze the transcriptional landscape.
To overcome the limitations of poly (A) RNA sequencing in capturing the full spectrum of RNA transcripts.
To investigate both protein-coding and noncoding RNA transcription within the nucleus.

Main Methods:

Development and application of nuclear-RNA sequencing (nucRNA-seq).
Isolation and sequencing of nuclear RNAs, encompassing both spliced and unspliced transcripts.
Quantification of nuclear RNA transcripts to assess transcriptional output.

Main Results:

nucRNA-seq enables the capture and quantification of unspliced and spliced transcripts from protein-coding genes.
The method effectively identifies nuclear-retained long noncoding RNAs, which are often missed by poly (A) selection.
Provides a more complete picture of the transcriptional landscape compared to conventional methods.

Conclusions:

Nuclear-RNA sequencing (nucRNA-seq) offers a more comprehensive approach to transcriptome analysis.
This technique enhances the understanding of transcriptional regulation by including pre-mRNA and noncoding RNAs.
nucRNA-seq is valuable for studying the full scope of gene expression, including regions not typically polyadenylated.