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

CAMP: a modular metagenomics analysis system for integrated multistep data exploration.

NAR genomics and bioinformatics·2026

Same author

A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.

Nature communications·2025

Same author

Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.

Nature biotechnology·2025

Same author

Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types.

bioRxiv : the preprint server for biology·2025

Same author

A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.

bioRxiv : the preprint server for biology·2025

Same author

A foundational model for in vitro fertilization trained on 18 million time-lapse images.

Nature communications·2025

Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026

Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026

Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026

Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026

Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026

Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 5, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data.

Dmitry Meleshko^1,2, Andrey D Prjbelski³, Mikhail Raiko⁴

¹Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, NY 10021, United States.

Bioinformatics (Oxford, England)

|January 23, 2024

Summary

This summary is machine-generated.

We developed cloudrnaSPAdes, a novel RNA-sequencing assembler. This tool accurately reconstructs full-length RNA isoforms from barcoded linked-read data, addressing limitations in current annotation pipelines for isoform discovery.

More Related Videos

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Related Experiment Videos

Last Updated: Jul 5, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Area of Science:

Transcriptomics
Bioinformatics
Computational Biology

Background:

Long-read RNA sequencing offers full-length isoform analysis, but can be low coverage.
Barcoded short-read RNA sequencing (e.g., 10x Genomics linked-reads) provides higher coverage for isoform studies.
Existing pipelines struggle with barcoded short-read data, especially with coverage gaps.

Purpose of the Study:

To present cloudrnaSPAdes, a novel RNA-sequencing assembler.
To enable the determination of expressed isoforms from barcoded linked-read data in a reference-free manner.
To overcome limitations of current annotation pipelines for isoform discovery using barcoded short-read RNA-seq.

Main Methods:

Development of cloudrnaSPAdes, a feature release of the SPAdes assembler.
Application of the assembler to barcoded RNA-seq linked-read data.
Reference-free assembly of full-length isoforms.

Main Results:

cloudrnaSPAdes accurately assembles full-length isoforms from barcoded RNA-seq data.
The tool demonstrates effectiveness on both simulated and real human datasets.
Successful isoform determination even for genes with high transcript diversity.

Conclusions:

cloudrnaSPAdes provides a valuable solution for isoform discovery using high-coverage barcoded RNA-seq data.
The tool addresses the challenge of analyzing fragmented molecular information from linked-read sequencing.
This advancement facilitates more comprehensive transcriptomic analysis and isoform annotation.