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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: Jun 11, 2025

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

Published on: September 7, 2022

Streamlining RNA Aptamer Selection via Unique Molecular Identifiers and High-Throughput Sequencing.

Dengwei Zhang^1,2, Yuqing Liu^1,2, Huidong Huang¹

¹The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.

Analytical Chemistry

|October 10, 2024

Summary

This summary is machine-generated.

We developed ID-SELEX, an efficient RNA aptamer selection method using unique molecular identifiers. This approach accelerates aptamer discovery for applications in cell imaging, drug delivery, and therapeutics.

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Last Updated: Jun 11, 2025

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

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Published on: September 7, 2022

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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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:

Biotechnology
Molecular Biology
Genomics

Background:

RNA aptamers offer advantages over DNA aptamers for applications like cell imaging and therapeutics due to their structural diversity, higher affinity, and specificity.
Traditional RNA aptamer selection methods are lengthy and require multiple screening rounds, hindering their broad application.

Purpose of the Study:

To introduce an efficient truncated selection method, ID-SELEX, for rapid RNA aptamer discovery.
To overcome the time-consuming nature of traditional aptamer selection processes.

Main Methods:

Developed ID-SELEX (Identification DNA-SELEX), incorporating unique molecular identifiers (UMIs) into each template.
Utilized high-throughput sequencing to analyze UMI-labeled aptamer candidates, mitigating PCR amplification bias.
Applied ID-SELEX to select aptamers targeting human colon cancer cells (HCT-8) and mouse myoblast cells (C2C12).

Main Results:

Successfully identified high-quality aptamers targeting HCT-8 cells in only two selection rounds.
Selected six RNA aptamers targeting C2C12 cells in a single selection round.
Demonstrated the efficiency and versatility of ID-SELEX across different cell lines and species.

Conclusions:

ID-SELEX enables rapid RNA aptamer screening using high-throughput sequencing and UMI labeling.
This method facilitates swift aptamer discovery for human and murine cell lines.
ID-SELEX offers a novel molecular tool with potential for biomedical research, clinical applications, and precision medicine.