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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.
The technique...
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Related Experiment Video

Updated: May 7, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations.

Cenny Taslim, Yuan Zhang, Genevieve C Kendall

    Biorxiv : the Preprint Server for Biology
    |January 7, 2025
    PubMed
    Summary

    RNA-SeqEZPZ is a new automated pipeline that simplifies RNA sequencing (RNA-Seq) analysis for researchers. It offers a user-friendly interface and command-line options for reproducible and efficient genomic data analysis.

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    Area of Science:

    • Genomics
    • Bioinformatics
    • Computational Biology

    Background:

    • RNA sequencing (RNA-Seq) analysis is crucial in genomic research but often time-consuming and challenging to standardize.
    • Many labs use in-house scripts, leading to reproducibility issues and bottlenecks in data analysis.
    • The decreasing cost of RNA sequencing experiments generates vast amounts of data requiring efficient analysis pipelines.

    Purpose of the Study:

    • To develop an automated, user-friendly pipeline for rigorous and reproducible RNA-Seq analysis.
    • To provide a solution that eliminates the need for programming or bioinformatics expertise for routine analysis.
    • To offer flexibility for advanced users through command-line execution and customization.

    Main Methods:

    • Developed RNA-SeqEZPZ, an automated pipeline with a point-and-click interface and command-line options.
    • Implemented the pipeline using bash/SLURM and Nextflow for broad compatibility.
    • Integrated quality control, alignment, filtering, read counting, differential expression, and pathway analysis.
    • Included an interactive R shiny visualization tool and packaged all tools in a Singularity image for ease of installation and replicability.
    • Incorporated batch adjustment for minimizing technical variation effects.

    Main Results:

    • RNA-SeqEZPZ enables comprehensive RNA-Seq analysis from raw reads to functional interpretation.
    • The pipeline ensures reproducibility through standardized steps and containerization (Singularity).
    • Interactive visualizations facilitate the comparison of differentially expressed genes and pathways across experimental conditions.

    Conclusions:

    • RNA-SeqEZPZ significantly reduces the time and expertise required for RNA-Seq data analysis.
    • The pipeline enhances standardization and reproducibility in genomic research.
    • It empowers researchers to conduct complex RNA-Seq analyses efficiently and effectively.