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Related Concept Videos

RNA-seq03:21

RNA-seq

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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...
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Ribosome Profiling02:24

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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
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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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Related Experiment Video

Updated: Jan 11, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
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THRAISE: An automated and reproducible web platform for RNA-seq analysis.

Hyeon Ho Heo1, Soo-Jong Um1

  • 1Department of Integrative Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea.

Molecules and Cells
|November 15, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces a streamlined web platform for RNA-sequencing (RNA-seq) analysis, making complex bioinformatics accessible without coding. The system provides comprehensive analysis from raw data to functional enrichment, ensuring reproducible results for researchers.

Keywords:
AutomationRNA-sequencing analysisTranscriptome-wide High-throughput RNA-sequencing Analysis Integrated SystemWeb platform

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput RNA sequencing (RNA-seq) generates vast amounts of data.
  • Complex bioinformatics pipelines often require specialized programming expertise.
  • Accessible tools are needed to democratize RNA-seq data analysis.

Purpose of the Study:

  • To present a streamlined, user-friendly web platform for comprehensive RNA-seq analysis.
  • To enable researchers without programming skills to perform complex RNA-seq analyses.
  • To provide reproducible and accessible RNA-seq data interpretation.

Main Methods:

  • Development of a web platform integrating quality control, alignment, and quantification.
  • Implementation of differential gene expression analysis and functional enrichment.
  • Inclusion of alternative workflows for low-replicate datasets (n=1) using transcripts per million (TPM).
  • Utilizes Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Reactome, and Gene Set Enrichment Analysis for functional enrichment.

Main Results:

  • The platform processes raw Sequence Read Archive data through a complete RNA-seq analysis pipeline.
  • Real-time monitoring and interactive visualizations enhance user experience.
  • Functional enrichment analysis is performed using multiple established databases.
  • An alternative workflow is available for datasets with limited replicates.

Conclusions:

  • The Transcriptome-wide High-throughput RNA-seq Analysis Integrated System simplifies complex RNA-seq analysis.
  • It empowers researchers of all skill levels to conduct reproducible genomic studies.
  • The platform enhances accessibility and efficiency in RNA-seq data interpretation.