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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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A guide to single-cell RNA sequencing analysis using web-based tools for non-bioinformatician.

Sagnik Yarlagadda1, Todd D Giorgio1

  • 1Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.

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This guide simplifies single-cell RNA sequencing (scRNA-seq) analysis for researchers without bioinformatics expertise. It introduces user-friendly tools and a detailed pipeline to make scRNA-seq data accessible to all scientists.

Keywords:
ScRNA‐seqbioinformaticscomputationonlinepipeline

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Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Single-cell RNA sequencing (scRNA-seq) is a powerful research tool.
  • scRNA-seq data analysis traditionally requires extensive bioinformatics expertise.
  • Barriers persist for non-bioinformaticians, including complex language and lack of guidance.

Purpose of the Study:

  • To introduce user-friendly web-based scRNA-seq analysis tools.
  • To provide a comprehensive, start-to-finish scRNA-seq analysis pipeline for researchers.
  • To enable researchers of all computational backgrounds to perform scRNA-seq analysis.

Main Methods:

  • Overview of popular web-based scRNA-seq analysis tools and their features.
  • Detailed description of an introductory scRNA-seq analysis pipeline.
  • Reference to companion video tutorials for practical guidance.

Main Results:

  • Identification and introduction of accessible web-based scRNA-seq tools.
  • A step-by-step pipeline designed for ease of use.
  • Empowerment of researchers to conduct scRNA-seq analysis independently.

Conclusions:

  • User-friendly tools and clear pipelines are crucial for democratizing scRNA-seq analysis.
  • Continued development of accessible resources is needed to overcome remaining barriers.
  • This work aims to bridge the gap between scRNA-seq technology and broader research accessibility.