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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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Do it yourself! - Initial experiences with self-synthesized CsTFA for RNA-SIP analyses.

Severin Weis1, Susanne Jacksch1, Marius Welkerling1

  • 1Microbiology and Hygiene Group, Institute of Precision Medicine, Faculty of Medical & Life Sciences, Furtwangen University, Villingen-Schwenningen, Germany.

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|February 8, 2022
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Summary

Researchers developed a simple protocol to synthesize Cesium trifluoroacetate (CsTFA), a key medium for RNA Stable Isotope Probing (RNA-SIP). Self-made CsTFA effectively separates labeled and unlabeled bacterial RNA, matching commercial standards.

Keywords:
Density gradientMicrobial ecologyRNAStable Isotope ProbingUltracentrifugation

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Biochemistry

Background:

  • Cesium trifluoroacetate (CsTFA) is crucial for isopycnic centrifugation in RNA-based Stable Isotope Probing (RNA-SIP).
  • RNA-SIP links microbial community structure and function by analyzing RNA.
  • A reliable and accessible CsTFA synthesis method is needed.

Purpose of the Study:

  • To develop an easy protocol for synthesizing Cesium trifluoroacetate (CsTFA).
  • To evaluate the performance of self-synthesized CsTFA in RNA-SIP applications.
  • To compare self-synthesized CsTFA with commercially available CsTFA.

Main Methods:

  • Synthesis of CsTFA from cesium carbonate (Cs2CO3) and trifluoroacetic acid (TFA).
  • Isopycnic centrifugation using self-synthesized and commercial CsTFA.
  • Separation and analysis of isotopically labeled and unlabeled bacterial RNA.

Main Results:

  • A straightforward protocol for CsTFA synthesis was successfully established.
  • Self-synthesized CsTFA demonstrated comparable performance to commercial CsTFA.
  • Effective separation of labeled and unlabeled bacterial RNA was achieved using self-made CsTFA.

Conclusions:

  • Self-synthesis of CsTFA provides a viable and cost-effective alternative to commercial sources.
  • The developed protocol facilitates the use of RNA-SIP for microbial community analysis.
  • This method supports research linking microbial community structure and function.