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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: Aug 12, 2025

Obtaining High Quality RNA from Single Cell Populations in Human Postmortem Brain Tissue

Obtaining High Quality RNA from Single Cell Populations in Human Postmortem Brain Tissue

Published on: August 6, 2009

High-Resolution RNA Sequencing from PFA-Fixed Microscopy Sections.

Hao Ji¹, Simon Besson-Girard¹, Peter Androvic¹

¹Systems Neuroscience Laboratory, Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Munich, Germany.

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

|January 30, 2023

Summary

This summary is machine-generated.

Researchers developed a new method for RNA sequencing from archived, paraformaldehyde-fixed (PFA) tissue sections. This technique retrieves cross-linked mRNA, enabling high-quality transcriptomic analysis of valuable historical samples.

Keywords:

Microdissection PFA-fixation RNA extraction RNA sequencing

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Last Updated: Aug 12, 2025

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RNA Isolation from Cell Specific Subpopulations Using Laser-capture Microdissection Combined with Rapid Immunolabeling

RNA Isolation from Cell Specific Subpopulations Using Laser-capture Microdissection Combined with Rapid Immunolabeling

Published on: April 11, 2015

Area of Science:

Molecular Biology
Genomics
Histology

Background:

Archived biological tissues, particularly paraformaldehyde (PFA)-fixed sections used in microscopy, present challenges for current RNA sequencing (RNA-seq) methods.
PFA fixation cross-links and protects RNA but also hinders its retrieval, limiting transcriptomic analysis of historical samples.

Purpose of the Study:

To develop a low-input RNA sequencing method compatible with archived PFA-fixed tissue sections.
To enable high-quality transcriptomic analysis and genomic analysis of PFA-fixed samples.

Main Methods:

A novel decrosslinking protocol utilizing Proteinase K activity was developed to retrieve PFA-cross-linked messenger RNAs (mRNAs).
The retrieved mRNAs were then processed using the Smart-seq2 library preparation protocol.
The method was validated using archived mouse brain sections prepared for imaging.

Main Results:

The developed protocol successfully yielded high-quality RNA sequencing results from archived PFA-fixed mouse brain sections.
The method allows for spatially defined transcriptomic analysis of archived sections.
The protocol inactivates pathogenic samples, enabling work under regular biosafety levels.

Conclusions:

This low-input RNA sequencing method effectively retrieves and analyzes RNA from archived PFA-fixed sections.
The protocol expands the utility of historical tissue samples for genomic and transcriptomic studies.
The method offers a safe and accessible approach for analyzing PFA-fixed specimens.