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...

You might also read

Related Articles

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

Sort by

Same author

Chemically synthesized, non-capped and non-polyadenylated peptide-coding RNA efficiently induces antigen-specific CD8<sup>+</sup> T cells.

Nature biomedical engineering·2026

Same author

Preclinical immunogenicity of the LP.8.1-adapted BNT162b2 COVID-19 vaccine.

NPJ vaccines·2026

Same author

A multifunctional g-C<sub>3</sub>N<sub>4</sub>@WO<sub>3</sub> hybrid nanocomposite for integrated SPE-UPLC-DAD determination and photocatalytic degradation of tetracycline hydrochloride.

RSC advances·2026

Same author

Tumor-naïve ctDNA detection with deep learning-enhanced error suppression for sensitive mutation calling.

Genome medicine·2026

Same author

Preclinical assessment of broadly neutralizing HIV-1 antibody BNT351 with optimized pharmacokinetics and potent antiviral activity.

iScience·2026

Same author

VariantMedium: sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental data.

Genome medicine·2026

Search research articles

Related Experiment Video

Updated: Apr 11, 2026

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Published on: May 16, 2020

In Silico HLA Typing Using Standard RNA-Seq Sequence Reads.

Sebastian Boegel¹, Jelle Scholtalbers, Martin Löwer

¹TRON gGmbH - Translational Oncology at Johannes Gutenberg-University Medical Center gGmbH Mainz, Langenbeckstr. 1, Building 708, Mainz, 55131, Germany, boegels@uni-mainz.de.

Methods in Molecular Biology (Clifton, N.J.)

|May 31, 2015

Summary

This study presents a novel method using RNA-Seq data to determine human leukocyte antigen (HLA) types and expression. The seq2HLA algorithm efficiently analyzes transcriptome sequencing reads for HLA profiling.

More Related Videos

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

Related Experiment Videos

Last Updated: Apr 11, 2026

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis

Published on: May 16, 2020

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

Published on: May 19, 2019

Area of Science:

Immunogenomics
Bioinformatics
Molecular Biology

Background:

Next-generation sequencing (NGS) and RNA-Seq are widely used for transcriptome profiling.
Human Leukocyte Antigen (HLA) typing is crucial for transplantation and disease association studies.
Existing HLA typing methods can be costly and time-consuming.

Purpose of the Study:

To describe a method for determining HLA class I and II types and expression from standard RNA-Seq data.
To introduce and validate the seq2HLA algorithm for HLA analysis.
To demonstrate the utility of RNA-Seq for HLA imputation.

Main Methods:

Utilized standard RNA-Seq data, which generates billions of short sequence reads.
Developed and applied the seq2HLA algorithm for analyzing transcriptome sequencing reads.
Validated the method using a publicly available RNA-Seq dataset from the Raji cell line.

Main Results:

Successfully obtained human leukocyte antigen (HLA) class I and II types from RNA-Seq data.
Quantified HLA expression levels using the seq2HLA algorithm.
Demonstrated the feasibility and accuracy of HLA imputation from transcriptome sequencing.

Conclusions:

Standard RNA-Seq data can be leveraged for comprehensive HLA typing and expression analysis.
The seq2HLA algorithm provides an efficient and accessible tool for HLA profiling.
This method offers a cost-effective alternative for HLA characterization in research and clinical settings.