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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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PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources.

S Castillo-Lara1,2, E Pascual-Carreras1,2, J F Abril1,2

  • 1Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Catalonia, Spain.

Bioinformatics (Oxford, England)
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Summary

PlanExp is a new web tool for exploring planarian gene expression data from RNA sequencing. It aids researchers in understanding planarian regeneration and development by visualizing complex datasets.

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Area of Science:

  • Developmental Biology
  • Genomics
  • Systems Biology

Background:

  • The increasing volume of transcriptomic and genomic data from planarian research presents challenges in analysis.
  • Understanding planarian regeneration and development requires effective tools for data exploration and visualization.

Purpose of the Study:

  • To introduce PlanExp, a web application designed for exploring and visualizing gene expression data in planarians.
  • To facilitate the integration of diverse RNA sequencing (RNA-seq) data, including traditional and single-cell RNA-seq.

Main Methods:

  • Development of a web application, PlanExp, for interactive data visualization.
  • Integration with the PlanNET web application for linking expression data with sequence annotations.
  • Implementation of a gene/protein network editor and a network expression mapper.

Main Results:

  • PlanExp offers tools for creating interactive plots like heatmaps and scatterplots.
  • The application links gene expression data with genome and transcript-level annotations.
  • Features include genetic interaction prediction from single-cell RNA-seq and network expression mapping.

Conclusions:

  • PlanExp provides a valuable resource for researchers studying planarian biology.
  • The tool aims to bridge the gap between systems biology approaches and the study of planarian regeneration.