Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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 microarray-based...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Genetic Counseling for Childhood Cancer Predisposition Syndromes: A Six-Year Retrospective Study.

Children (Basel, Switzerland)·2026

Same author

Diagnostic Yield and Genotype-Phenotype Overlap in Pediatric Autism Spectrum Disorder Patients Using Whole-Exome Sequencing and Phenotype-Driven Variant Interpretation: A Single-Center Cohort Study.

Children (Basel, Switzerland)·2026

Same author

Clinical Utility of Multiplex Ligation-Dependent Probe Amplification in the Genetic Assessment of Patients with Myelodysplastic Syndrome.

Biomedicines·2025

Same author

A Novel Frameshift Variant in the SPAST Gene Causing Hereditary Spastic Paraplegia in a Bulgarian-Turkish Family.

Neurology international·2025

Same author

Genomic Evaluation of AML-Main Techniques and Novel Approaches.

Journal of clinical medicine·2025

Same author

An Ultra-Rare Disorder: Case Report on Cerebrotendinous Xanthomatosis.

Reports (MDPI)·2025

Search research articles

Related Experiment Video

Updated: Jun 26, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

A Lightweight Workflow for Targeted Long-Read Transcriptomic Profiling Using Oxford Nanopore Sequencing.

Mariya Levkova^1,2

¹Department of Medical Genetics, Medical University Varna, Marin Drinov Str. 55, 9000 Varna, Bulgaria.

Methods and Protocols

|June 25, 2026

Summary

This summary is machine-generated.

We developed a lightweight pipeline for targeted long-read RNA sequencing analysis using Oxford Nanopore Technologies (ONT) data. This reproducible workflow enables efficient gene expression profiling, even with limited computational resources.

Keywords:

FFPE transcriptomics Oxford Nanopore sequencing bioinformatics pipeline long-read transcriptomics targeted RNA sequencing

More Related Videos

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Cost-Efficient Transcriptomic-Based Drug Screening

Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

Related Experiment Videos

Last Updated: Jun 26, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Cost-Efficient Transcriptomic-Based Drug Screening

Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Long-read sequencing offers portability for small-scale studies.
Existing RNA-seq frameworks are resource-intensive and designed for whole-transcriptome analysis.

Purpose of the Study:

To present a lightweight, reproducible computational pipeline for targeted long-read transcriptomic profiling.
To enable efficient analysis of Oxford Nanopore Technologies (ONT) cDNA sequencing data.

Main Methods:

Development of a computational pipeline for targeted alignment of ONT cDNA sequencing data.
Utilized minimap2 for alignment to a custom transcript reference panel.
Implemented reads-per-million (RPM) for gene-level read counting and normalization.

Main Results:

Successfully evaluated the pipeline on FFPE colorectal carcinoma samples (MSI-high).
Enabled rapid quantification of mismatch repair gene expression and detection of immune markers (CD8A, PDCD1, HAVCR2).
Demonstrated applicability across multiplexed barcode samples.

Conclusions:

The pipeline offers a simple, reproducible, and computationally efficient framework for targeted transcriptomic analysis.
Facilitates the adoption of ONT-based transcriptomic profiling in resource-constrained environments.