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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 26, 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

Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.

Xiaofeng Wu^1,2, Weize Xu^1,2, Lulu Deng^1,2

¹State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.

Nature Biomedical Engineering

|May 14, 2024

Summary

This summary is machine-generated.

We developed multi-omics in situ pairwise sequencing (MiP-seq) for simultaneous DNA, RNA, and protein detection at subcellular resolution. This technology enhances discovery of cellular functions and disease mechanisms with reduced costs.

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Last Updated: Jun 26, 2025

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Published on: July 6, 2022

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Spatial multi-omics technologies are crucial for understanding cellular functions and disease mechanisms.
Existing in situ sequencing methods have limitations in decoding capacity and cost.

Purpose of the Study:

To develop and demonstrate the applicability of multi-omics in situ pairwise sequencing (MiP-seq).
To enable simultaneous detection of DNA, RNA, proteins, and biomolecules at subcellular resolution.

Main Methods:

Development of MiP-seq, a novel in situ sequencing technique.
Integration of MiP-seq with in vivo calcium and Raman imaging.
Application of a sequential dilution strategy for resolving crowded signals.

Main Results:

MiP-seq enhances decoding capacity and reduces sequencing and imaging costs compared to other methods.
MiP-seq effectively detects gene mutations, allele-specific expression, and RNA modifications.
A spatial multi-omics atlas of mouse brain tissues was generated, correlating gene expression with neuronal activity and biochemical fingerprints.

Conclusions:

MiP-seq offers a powerful, cost-effective approach for high-throughput spatial multi-omics analysis.
This technology facilitates multidimensional analysis of molecular and functional tissue maps.
MiP-seq advances the study of cellular functions and disease mechanisms at subcellular resolution.