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Related Concept Videos

RNA-seq03:21

RNA-seq

12.1K
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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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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RNA Stability01:53

RNA Stability

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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RNA Splicing01:32

RNA Splicing

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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...
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RNA Editing02:23

RNA Editing

9.9K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Updated: Feb 5, 2026

Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
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Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs

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Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure.

Kapeel M Chougule1, Liya Wang1, Joshua C Stein1

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

Current Protocols in Bioinformatics
|September 1, 2018
PubMed
Summary
This summary is machine-generated.

New RNA-seq analysis protocols simplify gene expression studies. These user-friendly graphical tools on CyVerse Cyberinfrastructure enhance accessibility for researchers, improving scalability and accuracy in transcriptomic analysis.

Keywords:
CyVerseRNA-seqbioinformaticsdifferential gene expressiondiscovery environmentpseudo-alignment based transcript quantificationreference guided gene expressiontranscript assemblytuxedo protocol

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Area of Science:

  • Transcriptomics
  • Bioinformatics
  • Computational Biology

Background:

  • RNA sequencing (RNA-seq) is crucial for gene expression analysis.
  • Existing RNA-seq tools vary in performance, scalability, and ease of use.
  • Command-line interfaces of current tools pose challenges for many researchers.

Purpose of the Study:

  • To develop and validate user-friendly RNA-seq analysis protocols.
  • To deploy these protocols on CyVerse Cyberinfrastructure with graphical user interfaces.
  • To improve accessibility and usability of RNA-seq analysis for researchers.

Main Methods:

  • Development of two novel RNA-seq analysis protocols.
  • Deployment of all analytical tools on CyVerse Cyberinfrastructure.
  • Implementation of user-friendly graphical interfaces for protocol execution.
  • Validation of protocol performance using plant RNA-seq data.

Main Results:

  • The developed protocols offer user-friendly graphical interfaces, simplifying complex RNA-seq analysis.
  • Deployment on CyVerse Cyberinfrastructure ensures scalability and accessibility.
  • Validated performance demonstrates the utility of these new protocols for plant transcriptomics.
  • The protocols address the limitations of command-line-dependent tools.

Conclusions:

  • New graphical RNA-seq protocols on CyVerse enhance accessibility and ease of use.
  • These protocols provide scalable and accurate solutions for transcriptomic data analysis.
  • The findings facilitate broader adoption of RNA-seq analysis in research.
  • User-friendly interfaces are critical for democratizing advanced bioinformatics tools.