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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. 
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Related Experiment Video

Updated: May 5, 2026

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets
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A platform independent RNA-Seq protocol for the detection of transcriptome complexity.

Claudia Calabrese, Marina Mangiulli, Caterina Manzari

  • 1Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale delle Ricerche (CNR), Bari, Italy. apollonia.tullo@ba.itb.cnr.it.

BMC Genomics
|December 7, 2013
PubMed
Summary

Researchers developed a novel, platform-independent protocol for strand-specific cDNA library preparation. This method enables comprehensive transcriptome analysis across various next-generation sequencing technologies, even with low RNA input.

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Eukaryotic transcription is highly complex, with most of the genome transcribed into various RNA species, including non-coding RNAs.
  • Detecting all RNA species via high-throughput transcriptome sequencing requires careful cDNA library construction.
  • Existing protocols often limit library utilization to a single sequencing platform.

Purpose of the Study:

  • To develop a versatile and efficient protocol for strand-specific cDNA library generation.
  • To enable comprehensive transcriptome analysis across different next-generation sequencing (NGS) platforms.
  • To provide a bioinformatics tool for analyzing sequencing data generated by the protocol.

Main Methods:

  • A unique protocol for generating and amplifying strand-specific cDNA libraries was established.
  • The protocol is designed for compatibility with major NGS platforms (e.g., Roche 454, Illumina, ABI/SOLiD).
  • The method accommodates low input total RNA quantities and is reproducible and fast.

Main Results:

  • The developed protocol generates a cDNA library representative of all RNA species.
  • The method is compatible with multiple major sequencing platforms, demonstrating platform independence.
  • A bioinformatics tool was developed for sequence analysis specific to this protocol.

Conclusions:

  • The protocol allows simultaneous analysis of the same sample using different NGS technologies.
  • This platform-independent strategy provides an accurate quantitative and qualitative portrait of complex whole transcriptomes.
  • The method is reproducible, fast, easy-to-perform, and effective even with low RNA input.