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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 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.
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Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
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Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

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Transcriptome Sequencing for the Detection of Chimeric Transcripts.

Hsueh-Ting Chu1,2

  • 1Department of Computer Science and Information Engineering, Asia University, No. 500, Liufeng Road, Wufeng District, Taichung City, 413, Taiwan. htchu@asia.edu.tw.

Methods in Molecular Biology (Clifton, N.J.)
|December 16, 2015
PubMed
Summary
This summary is machine-generated.

Chimeric transcripts in cancer cells can be biomarkers and therapeutic targets. This study discusses detection methods using high-throughput sequencing, including assembly-based and alignment-based approaches for analyzing short read sequence data.

Keywords:
Cancer genesChimeric transcriptDe novo assemblyFusion genesTranscriptome sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Biology

Background:

  • Chimeric transcripts are observed in various cancer cells.
  • These transcripts are potential biomarkers and therapeutic targets.
  • High-throughput sequencing technologies enable investigation of chimeric transcripts and associated gene expression.

Purpose of the Study:

  • To discuss methods for detecting chimeric transcripts.
  • To highlight the role of sequencing technologies in understanding genomic variations and interactions.

Main Methods:

  • Review of detection methods for chimeric transcripts from short read sequence data.
  • Discussion of assembly-based and alignment-based approaches.

Main Results:

  • Chimeric transcripts are detectable using modern sequencing technologies.
  • Both assembly-based and alignment-based methods are applicable for their investigation.

Conclusions:

  • Detection methods for chimeric transcripts are crucial for cancer research.
  • Understanding chimeric transcripts aids in identifying genomic structural variations and interactions.