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Development of Analytical Methods01:21

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An analytical methodology can be divided into four sequential steps: technique, method, procedure, and protocol. A technique is a scientific principle that rationalizes a specific phenomenon through chemical measurements. Adapting a technique for analyzing a sample of interest is termed a method. The procedure outlines the directions for performing the analysis via an analytical method. The protocol is the detailed guidelines on the procedure, which should be strictly followed to obtain the...
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In certain chromatographic separations, solutes transfer between the mobile phase and the stationary phase via sorption, which typically refers to the process of adsorption. For many chromatographic systems, the sorption process often depends on the polarity of the compounds—an expression of the overall dipole moment within the molecule. During the separation process, there is competition between the solute and solvent for adsorption to the stationary phase. Highly polar compounds and...
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An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci
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exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Joel Rozowsky1, Robert R Kitchen1, Jonathan J Park1

  • 1Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Cell Systems
|April 9, 2019
PubMed
Summary
This summary is machine-generated.

Analyzing extracellular RNAs (exRNAs) in biofluids is challenging. The exceRpt toolkit offers a robust solution for processing exRNA sequencing data, ensuring reliable quality control and abundance estimates.

Keywords:
RNA sequencingRNA-seqbioinformaticsbioinformatics toolexRNAsextracellular RNAgenomicspipelinetranscriptome

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OLIgo Mass Profiling OLIMP of Extracellular Polysaccharides
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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Small RNA sequencing is crucial for studying extracellular RNAs (exRNAs) in biofluids.
  • exRNA analysis faces challenges including contamination, low concentrations, and exogenous RNA.
  • Standardized analysis is needed for reproducible exRNA research.

Purpose of the Study:

  • To introduce exceRpt, a novel toolkit for processing extracellular RNA sequencing data.
  • To provide a standardized computational framework for exRNA analysis.
  • To enhance the reliability and interpretability of exRNA sequencing results.

Main Methods:

  • exceRpt employs a cascade of filters and quantifications, prioritizing annotated RNAs.
  • The toolkit generates quality control reports and quantifies RNA biotype abundance.
  • It characterizes mappings to exogenous genomes for phylogenetic analysis.

Main Results:

  • exceRpt successfully processed approximately 3,500 exRNA-seq datasets in the public exRNA Atlas.
  • The toolkit provides robust quality control and abundance estimates for diverse RNA types.
  • It enables the identification and characterization of exogenous RNA sources.

Conclusions:

  • exceRpt addresses key challenges in exRNA sequencing analysis.
  • The toolkit facilitates standardized and reliable processing of exRNA data.
  • exceRpt is a valuable resource for the Extracellular RNA Communication Consortium and the broader research community.