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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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lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

Michael B Clark1, Tim R Mercer2, Giovanni Bussotti3

  • 11] Garvan Institute of Medical Research, Sydney, Australia. [2] MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK.

Nature Methods
|March 10, 2015
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Summary

Capture sequencing (CaptureSeq) excels at detecting and quantifying low-expression genes, offering accurate differential expression measurements and minimal technical variation compared to qRT-PCR and RNA-seq.

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Area of Science:

  • Genomics and Transcriptomics
  • Molecular Biology

Background:

  • Accurate assembly and quantification of long noncoding RNAs (lncRNAs) and novel coding exons are crucial for comprehensive genome annotation.
  • Existing methods like quantitative RT-PCR (qRT-PCR) and RNA-sequencing (RNA-seq) have limitations in detecting and quantifying low-expression transcripts.

Purpose of the Study:

  • To compare the efficacy of quantitative RT-PCR (qRT-PCR), RNA-seq, and capture sequencing (CaptureSeq) for analyzing lncRNAs and novel coding exons.
  • To evaluate the performance of these methods across diverse human tissues for gene expression profiling.

Main Methods:

  • Comparative analysis of three distinct transcriptomic profiling techniques: qRT-PCR, RNA-seq, and CaptureSeq.
  • Application of these methods to RNA samples from 20 distinct human tissues.
  • Assessment of transcript assembly, quantification accuracy, and technical variation.

Main Results:

  • CaptureSeq demonstrated superior performance in the detection and quantification of genes with low expression levels.
  • CaptureSeq exhibited minimal technical variation, ensuring reliable and reproducible measurements.
  • The study confirmed CaptureSeq's accuracy in measuring differential gene expression across tissues.

Conclusions:

  • CaptureSeq is a highly effective method for comprehensive transcriptomic analysis, particularly for low-abundance transcripts.
  • This approach refines and expands existing genomic annotations and facilitates the creation of detailed gene expression atlases.
  • CaptureSeq offers a robust solution for discovering and quantifying novel coding exons and lncRNAs.