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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: Jun 18, 2025

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Published on: August 14, 2018

Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.

Hower Lee¹, Christoffer Mattsson Langseth¹, Sergio Marco Salas¹

¹Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65 Solna, Sweden.

Development (Cambridge, England)

|August 5, 2024

Summary

We developed a new method for mapping gene activity within tissues, enabling detailed cellular and tissue analysis. This approach offers high throughput and multiplexing for diverse biological research.

Keywords:

In situ hybridization Multi-omics Multiplex imaging Open source Padlock probes Spatial transcriptomics

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Last Updated: Jun 18, 2025

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Visualizing Genetic Variants, Short Targets, and Point Mutations in the Morphological Tissue Context with an RNA In Situ Hybridization Assay

Published on: August 14, 2018

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Multiplexed spatial profiling of messenger RNAs (mRNAs) is crucial for understanding tissue architecture and cellular diversity.
Existing methods face challenges in sensitivity, throughput, and multiplexing capabilities.

Purpose of the Study:

To introduce a novel, sensitive, open-source method for generating in situ expression maps of hundreds of genes.
To provide a flexible and high-throughput approach for spatially resolved transcriptomics.

Main Methods:

Direct ligation of padlock probes on mRNAs.
Rolling circle amplification for signal enhancement.
Hybridization-based in situ combinatorial barcoding for large multiplexing.

Main Results:

Achieved high detection efficiency and high-throughput gene expression mapping.
Validated the method across multiple species.
Demonstrated compatibility with orthogonal methods like antibody staining.

Conclusions:

The developed method facilitates high-throughput spatially resolved transcriptomics.
It offers a valuable tool for developmental and tissue biology studies.
An end-to-end computational workflow is provided to support diverse applications.