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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: Jul 15, 2025

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing.

Yuchao Xia^1,2, Zijie Jin^3,4, Chengsheng Zhang²

¹College of Science, Beijing Information Science and Technology University, 100192, Beijing, China.

Nature Communications

|September 23, 2023

Summary

This summary is machine-generated.

We developed TAGET, a computational toolkit for analyzing full-length transcriptome data from Iso-seq (Isoform Sequencing). TAGET improves the discovery of novel isoforms and gene fusions, identifying ECM1b as a potential tumor suppressor.

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Last Updated: Jul 15, 2025

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

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Published on: April 8, 2017

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Published on: August 4, 2016

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Single-molecule Real-time Isoform Sequencing (Iso-seq) offers long, accurate reads ideal for full-length transcriptome analysis.
Analyzing Iso-seq data requires specialized computational tools for comprehensive insights.

Purpose of the Study:

To introduce TAGET, an integrated computational toolkit for Iso-seq data analysis.
To enhance transcript alignment, annotation, gene fusion detection, and quantification, including differential expression and isoform usage analysis.

Main Methods:

Development of the TAGET computational toolkit.
Evaluation using public and patient-derived Iso-seq datasets.
Experimental validation of key findings, including gene fusion and differential isoform usage.

Main Results:

TAGET provides more precise novel splice site prediction compared to existing methods.
TAGET enables more accurate discovery of novel isoforms and gene fusions.
Identification and experimental validation of ECM1 differential isoform usage, with ECM1b implicated as a potential tumor suppressor in laryngocarcinoma.

Conclusions:

TAGET is a valuable computational toolkit for full-length transcriptome studies.
The toolkit facilitates accurate analysis of Iso-seq data, leading to significant biological discoveries.
TAGET aids in identifying potential therapeutic targets, such as ECM1b in cancer.