Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

12.2K
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...
12.2K
Ribosome Profiling02:24

Ribosome Profiling

4.2K
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...
4.2K

You might also read

Related Articles

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

Sort by
Same author

Convergence and divergence of DNA methylation and gene expression patterns in neopolyploid Arabidopsis kamchatica.

Nature communications·2026
Same author

Tonotopic specialization of MYO7A isoforms in auditory hair cells.

Nature communications·2026
Same author

Hybrid untargeted short-read and targeted long-read RNA sequencing facilitates genotype-phenotype associations at single-cell resolution.

Genome biology·2026
Same author

Multi-sample, multi-platform isoform quantification using empirical Bayes.

bioRxiv : the preprint server for biology·2026
Same author

Resolving Sialylated N-Glycans and Immune Cell Landscapes Using a Unified Same-Section IMC-MSI Workflow.

bioRxiv : the preprint server for biology·2026
Same author

eSIG-Net: an interaction language model that decodes the protein code of single mutations.

Nature methods·2026

Related Experiment Video

Updated: Feb 28, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

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

Published on: November 7, 2025

443

A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification.

David Wissel1,2,3, Madison M Mehlferber4,5, Khue M Nguyen6

  • 1Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.

Genome Biology
|February 26, 2026
PubMed
Summary
This summary is machine-generated.

PacBio Kinnex long-read RNA sequencing offers reliable full-length transcript quantification, improving accuracy over short-read methods for complex genes. This platform enhances transcript discovery and quantification in large-scale studies.

Keywords:
Endothelial cellsLong-read RNA-seqPacBioQuantification

More Related Videos

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
05:12

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

1.4K
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

11.0K

Related Experiment Videos

Last Updated: Feb 28, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

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

Published on: November 7, 2025

443
Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms
05:12

Author Spotlight: AQRNA-seq Role in Mapping Small RNAs and Unraveling Protein Translation Mechanisms

Published on: February 2, 2024

1.4K
Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

11.0K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • RNA sequencing (RNA-seq) struggles with assembling fragmented reads, especially for complex genes, leading to transcript discovery and quantification errors.
  • PacBio long-read RNA sequencing provides clearer transcript resolution than short-read technologies.
  • The PacBio Kinnex platform uses cDNA concatenation to boost read yield but requires quantitative performance evaluation at scale.

Purpose of the Study:

  • To benchmark the quantitative performance of the high-throughput PacBio Kinnex platform against Illumina short-read RNA-seq.
  • To evaluate transcript discovery and quantification accuracy, especially for complex genes.
  • To identify optimal long-read analysis tools for Kinnex data.

Main Methods:

  • Matched, deeply sequenced datasets from endothelial cell differentiation time course.
  • Benchmarking PacBio Kinnex long-read RNA-seq against Illumina short-read RNA-seq.
  • Evaluation of transcript discovery and quantification accuracy, including differential transcript expression.
  • Benchmarking of long-read analysis tools, including Oarfish.

Main Results:

  • Kinnex achieves comparable gene-level quantification and superior transcript discovery and quantification accuracy compared to Illumina.
  • Illumina detects more transcripts, but many are potentially unstable or ambiguous in complex genes.
  • Kinnex provides more reliable differential transcript expression calls, with a minor bias against short transcripts (<1.25 kb).
  • Kinnex and Illumina quantifications show high concordance when Illumina data is corrected for inferential variability.
  • Oarfish is identified as an efficient tool for analyzing Kinnex data.

Conclusions:

  • The PacBio Kinnex platform is established as a reliable tool for full-length transcript quantification.
  • Kinnex enhances the accuracy of transcript discovery and quantification, particularly for complex transcriptomes.