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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 Profiling02:24

Ribosome Profiling

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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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

Mattia D'Antonio, Paolo D'Onorio De Meo, Matteo Pallocca

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    Summary
    This summary is machine-generated.

    Researchers can now analyze complex RNA-Seq data with RAP, a user-friendly cloud application. This RNA-Seq Analysis Pipeline simplifies gene expression, splicing, and polyadenylation analysis without requiring advanced bioinformatics skills.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Next Generation Sequencing (NGS) has revolutionized RNA studies, enabling detailed analysis of RNA-Seq data.
    • Transcriptome complexity and regulatory pathways present significant challenges in RNA-Seq data analysis.

    Purpose of the Study:

    • To develop an effective and user-friendly cloud-based web application for comprehensive RNA-Seq data analysis.
    • To integrate state-of-the-art bioinformatics tools and custom scripts into a modular analysis workflow.

    Main Methods:

    • RNA-Seq Analysis Pipeline (RAP) integrates tools for quality control (FastQC, NGS QC Toolkit), gene/transcript quantification (Tophat, Cufflinks, HTSeq), alternative splicing detection (SpliceTrap), and chimeric transcript identification (ChimeraScan).
    • Custom modules identify splicing junctions and polyadenylation sites, while Cuffdiff2 and DESeq enable statistical analysis of expression, splicing, and polyadenylation.
    • The workflow is executed on a cloud computing environment via a user-friendly web interface.

    Main Results:

    • RAP provides a customizable and automated RNA-Seq analysis workflow accessible through a web interface.
    • Users can perform complex analyses without requiring specialized bioinformatics or IT expertise.
    • The application generates tabular and graphical outputs for data browsing, filtering, and export.

    Conclusions:

    • RAP offers a comprehensive, modular, and accessible solution for RNA-Seq data analysis.
    • The platform empowers researchers by simplifying access to advanced bioinformatics tools and computational resources.
    • This facilitates deeper insights into transcriptome complexity and gene regulation.