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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 Profiling02:24

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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.
Applications of ribosome profiling
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Related Experiment Video

Updated: Oct 27, 2025

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
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A Modified Low-quantity RNA-Seq Method for Microbial Community and Diversity Analysis Using Small Subunit Ribosomal

Yong-Wei Yan1, Ting Zhu1, Bin Zou1

  • 1Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China.

Bio-Protocol
|July 21, 2021
PubMed
Summary

We developed a new RNA sequencing method for analyzing microbial communities using small subunit ribosomal RNA (SSU rRNA). This technique requires minimal RNA input and avoids DNA removal, enabling deeper insights into microbial diversity and active communities.

Keywords:
Low quantityMicrobial communityOTURNA-SeqSSU rRNA

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Bioinformatics

Background:

  • Small subunit ribosomal RNA (SSU rRNA) sequencing is crucial for microbial community analysis.
  • Existing methods often require high RNA input and DNA removal steps, limiting their application.
  • Accurate assessment of microbial diversity and active communities is essential for environmental and clinical studies.

Purpose of the Study:

  • To introduce a modified RNA sequencing (RNA-Seq) method for SSU rRNA-based microbial community analysis.
  • To enable low-input RNA analysis without DNA contamination.
  • To improve the accuracy and depth of microbial community and diversity profiling.

Main Methods:

  • Direct ligation of a 5' adaptor to RNA prior to reverse transcription.
  • Utilizing low-input RNA quantities (10-100 ng).
  • Omitting the DNA removal step in the workflow.

Main Results:

  • Obtained increased 16S rRNA sequences from specific variable regions (V1-V2) without DNA interference.
  • Enabled accurate operational taxonomic unit (OTU)-based microbial community and diversity analysis.
  • Generated SSU rRNA sequences suitable for bacterial universal primer coverage evaluation.

Conclusions:

  • The modified RNA-Seq method is effective for analyzing microbial communities using SSU rRNA.
  • This approach allows for the determination of potentially active microbial community structures and diversity in environmental samples.
  • The method facilitates the identification of novel microbial taxa and improves microbial profiling accuracy.