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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: Dec 23, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

Effective microtissue RNA extraction coupled with Smart-seq2 for reproducible and robust spatial transcriptome

Miki Yamazaki^1,2, Masahito Hosokawa^3,4, Koji Arikawa⁴

¹Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.

Scientific Reports

|April 29, 2020

Summary

This study presents a new method for spatial transcriptomics, ensuring tissue morphology and RNA stability for reproducible RNA sequencing. The technique effectively captures RNA from small samples, enabling detailed gene expression analysis in tissues.

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Last Updated: Dec 23, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

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Published on: July 6, 2022

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

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Published on: August 3, 2011

Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

Published on: November 18, 2014

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Spatial transcriptomics requires preserved tissue morphology and RNA integrity for reliable results.
Current methods face challenges in maintaining RNA stability during sample processing and collection.
Understanding molecular organization within tissues necessitates robust spatial transcriptomic techniques.

Purpose of the Study:

To develop a tissue processing method for reproducible RNA sequencing from microdissected samples.
To enhance RNA molecule stability and collection efficiency in fresh-frozen tissue specimens.
To enable high-quality spatial transcriptome analysis of small tissue samples.

Main Methods:

Dehydration fixation of fresh-frozen tissue to suppress RNA degradation.
Magnetic bead-based collection of small RNA quantities from microdissected samples.
Spatial transcriptome analysis of mouse liver and brain using serial microdissection (100 µm diameter, 10 µm thickness).

Main Results:

Prevention of RNA degradation at room temperature during sample processing.
Effective generation of sequencing libraries using Smart-seq2 from microdissected samples.
Reproducible sequence read mapping and detection of over 2000 genes compared to non-fixed samples.

Conclusions:

The developed method ensures robust and reproducible spatial transcriptomics by preserving RNA integrity and improving collection efficiency.
This technique is applicable to various transcriptome analyses, providing region-specific gene expression data from tissue specimens.
The method facilitates detailed insights into tissue molecular organization and cellular function in a morphological context.