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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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Using RNA-Seq for Transcriptome Profiling of Botrylloides sp. Regeneration.

Michael Meier1, Megan J Wilson2

  • 1Developmental Genomics Laboratory, Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.

Methods in Molecular Biology (Clifton, N.J.)
|April 1, 2022
PubMed
Summary
This summary is machine-generated.

RNA sequencing (RNA-Seq) enables transcriptome profiling in non-traditional models like Botrylloides leachii. This protocol details RNA-Seq analysis for identifying gene expression changes during regeneration and interpreting biological functions.

Keywords:
AscidianRNA-seqRegenerationSequencing

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Area of Science:

  • Marine Biology
  • Genomics
  • Developmental Biology

Background:

  • Decreasing sequencing costs and technological advancements facilitate transcriptomic studies in novel model organisms.
  • RNA sequencing (RNA-Seq) offers an unbiased approach for transcriptome profiling, identifying novel transcripts and isoforms.
  • Understanding gene expression dynamics is crucial for studying regeneration in organisms like the colonial ascidian Botrylloides leachii.

Purpose of the Study:

  • To present a comprehensive workflow for RNA sequencing data analysis in Botrylloides leachii.
  • To enable the detection and interpretation of differentially expressed genes during regeneration.
  • To provide a freely available, open-source protocol for transcriptomic analysis.

Main Methods:

  • Raw RNA sequencing reads processing and quality control.
  • Read mapping to a reference genome and de novo transcript assembly.
  • Quantification of transcript abundance and differential gene expression analysis.
  • Gene ontology enrichment analysis for biological interpretation.

Main Results:

  • Successful implementation of an RNA-Seq analysis pipeline for Botrylloides leachii.
  • Identification of a list of differentially expressed genes across different experimental conditions or developmental stages.
  • Biological interpretation of identified genes, revealing insights into regeneration mechanisms.

Conclusions:

  • The described RNA-Seq protocol provides a robust method for transcriptomic analysis in Botrylloides leachii.
  • This workflow facilitates the discovery of novel transcripts and the understanding of gene expression regulation during regeneration.
  • The open-source nature of the tools ensures accessibility and reproducibility for researchers studying non-traditional model organisms.