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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 24, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Detecting haplotype-specific transcript variation in long reads with FLAIR2.

Alison D Tang¹, Eva Hrabeta-Robinson¹, Roger Volden¹

¹Department of Biomolecular Engineering, University of California, Santa Cruz.

Biorxiv : the Preprint Server for Biology

|July 3, 2023

Summary

This summary is machine-generated.

Long-read sequencing enables simultaneous analysis of RNA variants and splicing, revealing ADAR

Keywords:

A-to-I editing ADAR FLAIR long-read RNA-seq

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Last Updated: Jul 24, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

RNA sequencing (RNA-Seq) reveals RNA processing aberrations linked to diseases.
Aberrant splicing and RNA single nucleotide variants (SNVs) impact transcript stability, localization, and function.
ADAR enzyme upregulation correlates with lung adenocarcinoma invasiveness and splicing regulation.

Approach:

Utilized long-read technology for full-length transcript sequencing.
Developed a computational workflow augmenting FLAIR to integrate RNA variant calls with isoforms.
Generated nanopore data from lung adenocarcinoma cells with and without ADAR knockdown.

Key Points:

Elucidated cis-effects of variants on splicing at a single molecule level.
Identified inosine-isoform associations to clarify ADAR's role in tumorigenesis.
Demonstrated long-read sequencing's capability to analyze RNA variants and splicing concurrently.

Conclusions:

Long-read sequencing provides valuable insights into RNA variant and splicing pattern relationships.
This approach enhances the understanding of RNA editing and splicing in disease contexts.