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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: May 5, 2026

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

Published on: August 5, 2020

High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow.

Xue Dong¹, Mengzhu Hu¹, Xiaonan Cui²

¹Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong 266101, China.

Genome Research

|August 5, 2025

Summary

We developed photocleavage and ligation sequencing (PCL-seq), a novel spatial transcriptomics method. This technique maps gene expression in tissues with subcellular resolution, applicable to both frozen and FFPE samples.

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Published on: August 5, 2020

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Published on: March 14, 2022

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Spatial heterogeneity in gene expression necessitates advanced spatial transcriptomics technologies.
Existing methods face limitations in tissue compatibility and resolution.

Purpose of the Study:

To introduce photocleavage and ligation sequencing (PCL-seq), a novel spatial transcriptomics method.
To demonstrate PCL-seq's utility in frozen and FFPE tissues with subcellular resolution.

Main Methods:

PCL-seq utilizes a light-controlled DNA labeling strategy with photocleavable oligonucleotides and ligation adapters.
Regions of interest (ROIs) are designated via microscopically controlled photo-illumination for targeted transcriptional profiling.
The method was applied to frozen mouse embryos and formalin-fixed paraffin-embedded (FFPE) mouse embryo sections.

Main Results:

PCL-seq generated spatially aligned gene expression matrices from frozen mouse embryos, detecting ~170,000 UMIs and 8600 genes (100 µm illumination).
The method successfully identified thousands of differentially enriched transcripts in FFPE mouse embryo sections (digits and vertebrae).
Subcellular resolution was achieved, enabling differential expression profiling between nuclear and cytoplasmic compartments.

Conclusions:

PCL-seq is an accessible and versatile workflow for spatial transcriptomic analysis.
The technology is compatible with both frozen and FFPE tissues.
PCL-seq provides high-quality data with subcellular resolution for detailed spatial gene expression studies.