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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: Nov 24, 2025

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry

Published on: April 21, 2022

Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS.

Pavlina Gregorova¹, Nina H Sipari², L Peter Sarin¹

¹RNAcious Laboratory, Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.

|December 28, 2020

Summary

A new ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method rapidly separates 50 modified ribonucleosides, including isomers, aiding RNA modification research.

Keywords:

C18 UPLC-MS post-transcriptional nucleoside modification quantification transfer RNA translation

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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Last Updated: Nov 24, 2025

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry

Characterizing RNA Modifications in Single Neurons Using Mass Spectrometry

Published on: April 21, 2022

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

Area of Science:

Biochemistry
Molecular Biology
Analytical Chemistry

Background:

Post-transcriptional RNA modifications are crucial for cellular metabolism and homeostasis.
Disturbances in RNA modifications are linked to various diseases, including diabetes and cancer.
Existing liquid chromatography-mass spectrometry (LC-MS) methods face challenges in resolving positional isomers and require long separation times.

Purpose of the Study:

To develop a faster and more efficient method for analyzing RNA modifications.
To improve the separation of modified ribonucleosides, including positional isomers.
To facilitate the study of RNA modification homeostasis in complex biological samples.

Main Methods:

Development of an ultra-performance LC-MS (UPLC-MS) method utilizing an octadecyl carbon chain (C18)-bonded silica matrix.
Achieved separation of 50 modified ribonucleosides in a single 9-min run.
Validated the method across different domains of life (Archaea, Bacteria, Eukarya) by analyzing tRNA modification patterns.

Main Results:

Efficient separation of 50 modified ribonucleosides, including positional isomers, within a 9-minute run.
Demonstrated method versatility by analyzing tRNA modifications in *Methanosarcina acetivorans*, *Pseudomonas syringae*, and *Saccharomyces cerevisiae*.
Method is amenable to stable isotope labeling and multiple reaction monitoring (MRM) for quantification.

Conclusions:

The developed UPLC-MS method is a fast and robust tool for broad-range exploration and quantification of ribonucleosides.
This method significantly reduces sample-to-sample turnover time for multisample analyses.
Facilitates future studies on RNA modification homeostasis in complex biological systems.