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-Seq09:54

RNA-Seq

73.5K
Among different methods to evaluate gene expression, the high-throughput sequencing of RNA, or RNA-seq. is particularly attractive, as it can be performed and analyzed without relying on prior available genomic information. During RNA-seq, RNA isolated from samples of interest is used to generate a DNA library, which is then amplified and sequenced. Ultimately, RNA-seq can determine which genes are expressed, the levels of their expression, and the presence of any previously unknown...
73.5K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

9.6K
This protocol outlines a comparative de novo transcriptome assembly and annotation workflow for novice bioinformaticians. The workflow is available for free entirely through CyVerse and connected by the Data Store. Command line and graphical user interfaces are used, but all code needed is available to copy and...
9.6K
RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells18:30

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

22.4K
This protocol presents a complete and detailed procedure to apply RNA-seq, a powerful next-generation DNA sequencing technology, to profile transcriptomes in human pulmonary microvascular endothelial cells with or without thrombin treatment. This protocol is generalizable to various cells or tissues affected by different reagents or disease...
22.4K
Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes05:07

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

356
This protocol allows initial quality control for RNA-seq experiments for wet-lab biologists with limited bioinformatics...
356
Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

18.1K
Galaxy and DAVID have emerged as popular tools that allow investigators without bioinformatics training to analyze and interpret RNA-Seq data. We describe a protocol for C. elegans researchers to perform RNA-Seq experiments, access and process the dataset using Galaxy and obtain meaningful biological information from the gene lists using...
18.1K
2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications05:41

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2.3K
Here, we describe a detailed protocol for an LC-MS-based sequencing method that can be used as a direct method to sequence short RNA (<35 nt per run) without a cDNA intermediate, and as a general method to sequence different nucleotide modifications in a single study at single-base...
2.3K

You might also read

Related Articles

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

Sort by
Same author

Real-time Targeted Enrichment in Single-cell Long-read Sequencing.

Genomics, proteomics & bioinformatics·2026
Same author

Technical feasibility of a long read, fourth generation sequencing platform in diagnostic profiling of clinical routine samples: a proof-of-concept study.

Pathologica·2026
Same author

A complete human pancreatic cancer genome.

bioRxiv : the preprint server for biology·2026
Same author

The complete genome of the KOLF2.1J reference iPSC line.

bioRxiv : the preprint server for biology·2026
Same author

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes.

bioRxiv : the preprint server for biology·2026
Same author

Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Jan 19, 2026

Next-Gen Transcriptomics Using RNA-Seq
09:54

Next-Gen Transcriptomics Using RNA-Seq

Published on: April 30, 2023

73.5K

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data.

Elena Bushmanova1, Dmitry Antipov1, Alla Lapidus1

  • 1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004, 6 linia V.O. 11d, Russia.

Gigascience
|September 9, 2019
PubMed
Summary

Generating large RNA-sequencing datasets requires robust transcriptome assemblers. The novel rnaSPAdes tool demonstrates superior performance in assembling genes and isoforms with high accuracy compared to existing methods.

Keywords:
de novo assemblyRNA-Seqtranscriptome assembly

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.6K
RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
18:30

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

Published on: February 13, 2013

22.4K

Related Experiment Videos

Last Updated: Jan 19, 2026

Next-Gen Transcriptomics Using RNA-Seq
09:54

Next-Gen Transcriptomics Using RNA-Seq

Published on: April 30, 2023

73.5K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.6K
RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
18:30

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

Published on: February 13, 2013

22.4K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Advancements in RNA-sequencing enable large dataset generation.
  • Reference-based and de novo transcriptome assemblers have limitations.
  • De novo transcriptome reconstruction from short reads is challenging due to biological complexities.

Purpose of the Study:

  • Introduce rnaSPAdes, a novel transcriptome assembler.
  • Evaluate rnaSPAdes performance against existing tools.
  • Provide quality assessment for rnaSPAdes assemblies.

Main Methods:

  • Developed rnaSPAdes based on the SPAdes genome assembler.
  • Explored computational parallels between transcriptome and single-cell genome assembly.
  • Compared rnaSPAdes with other assemblers using multiple evaluation approaches on diverse RNA-sequencing datasets.

Main Results:

  • Presented quality assessment reports for rnaSPAdes.
  • Highlighted strengths and weaknesses of various assemblers.
  • rnaSPAdes typically assembled more genes and isoforms with higher accuracy than competitors on average.

Conclusions:

  • No single assembler is superior across all metrics and datasets.
  • rnaSPAdes shows strong performance in gene and isoform assembly.
  • rnaSPAdes offers competitive accuracy in transcriptome reconstruction.