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Related Concept Videos

RNA-seq03:21

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 microarray-based...
Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
Pre-mRNA Processing: RNA Splicing01:32

Pre-mRNA Processing: RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...

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Related Experiment Video

Updated: May 8, 2026

Large-scale Production of Recombinant RNAs on a Circular Scaffold Using a Viroid-derived System in Escherichia coli
10:38

Large-scale Production of Recombinant RNAs on a Circular Scaffold Using a Viroid-derived System in Escherichia coli

Published on: November 30, 2018

L_RNA_scaffolder: scaffolding genomes with transcripts.

Wei Xue1, Jiong-Tang Li, Ya-Ping Zhu

  • 1The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. lijt83@gmail.com.

BMC Genomics
|September 10, 2013
PubMed
Summary

L_RNA_scaffolder utilizes long transcriptome reads for efficient genome scaffolding, improving N50 length and transcript coverage. This novel method simplifies genome assembly compared to traditional mate-pair libraries.

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

Last Updated: May 8, 2026

Large-scale Production of Recombinant RNAs on a Circular Scaffold Using a Viroid-derived System in Escherichia coli
10:38

Large-scale Production of Recombinant RNAs on a Circular Scaffold Using a Viroid-derived System in Escherichia coli

Published on: November 30, 2018

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

Area of Science:

  • Genomics
  • Bioinformatics
  • Transcriptomics

Background:

  • De novo genome assembly requires large mate-pair libraries, which are complex and time-consuming.
  • Existing methods struggle to increase contiguity (N50 length) in complex genomes, leading to poor transcript coverage.
  • There is a need for simpler scaffolding approaches to improve transcript elongation.

Purpose of the Study:

  • To introduce L_RNA_scaffolder, a novel genome scaffolding method.
  • To demonstrate the method's accuracy and effectiveness in improving genome assembly contiguity and transcript coverage.

Main Methods:

  • L_RNA_scaffolder uses long transcriptome reads to order, orient, and combine genomic fragments.
  • The method was tested on zebrafish and human genomes using transcriptome data.
  • Application to a pearl oyster draft genome was also performed.

Main Results:

  • Scaffolding the zebrafish genome demonstrated the method's accuracy.
  • Human genome N50 was doubled, outperforming existing mate-pair library scaffolders.
  • Near-complete transcript coverage was achieved, particularly for long transcripts.
  • Significant increase in gene model length observed in the pearl oyster genome.

Conclusions:

  • L_RNA_scaffolder offers a simple and high-throughput genome scaffolding solution using RNA-seq data.
  • The method effectively improves genome assembly contiguity and transcript coverage.
  • L_RNA_scaffolder is publicly available for researchers.