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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 9, 2025

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

TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline.

Maxfield M G Kelsey¹, Radha L Kalekar¹, John M Sedivy¹

¹Center on the Biology of Aging, and the Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States.

Biorxiv : the Preprint Server for Biology

|October 28, 2024

Summary

This summary is machine-generated.

The TE-Seq pipeline analyzes RNA and DNA sequencing data to study transposable elements (TEs), also known as the

Keywords:

Long read DNA-Seq Polymorphic loci RNA-Seq Retrotransposable elements Transposable elements

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Last Updated: Jun 9, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Published on: August 4, 2016

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

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Published on: September 13, 2018

Area of Science:

Genomics and Bioinformatics
Molecular Biology
Evolutionary Biology

Background:

Transposable elements (TEs) are increasingly recognized for their significant roles in biological processes.
Analyzing the mobile 'dark genome' of TEs requires specialized computational approaches.
Existing methods may not fully capture the complexity of TE expression and genomic contribution.

Purpose of the Study:

To introduce the TE-Seq pipeline for comprehensive analysis of both genes and transposable elements (TEs) in sequencing data.
To enable detailed examination of TE expression at individual element and clade levels.
To facilitate the construction of TE-complete genomes using long-read DNA sequencing data for functional characterization.

Main Methods:

End-to-end analysis of RNA-sequencing data using the TE-Seq pipeline.
Implementation of current computational methods specifically designed for transposable element analysis.
Integration of long-read DNA sequencing data to identify and incorporate non-reference TE loci.

Main Results:

The TE-Seq pipeline provides a comprehensive analysis of both gene and transposable element expression.
It allows for high-resolution analysis of TE expression at both individual element and TE clade levels.
The pipeline generates TE-complete genomes, including polymorphic TE-loci from long-read data.

Conclusions:

The TE-Seq pipeline offers a robust solution for studying the 'dark genome' of transposable elements.
It enhances the functional characterization of evolutionarily young mobile elements.
This approach advances the comprehensive analysis of genomic and transcriptomic data concerning TEs.