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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
Published on: August 4, 2016
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RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets.
Guorong Xu1, Michael J Strong2, Michelle R Lacey3
1Department of Computer Science, University of New Orleans Lakefront, New Orleans, Louisiana, United States of America.
Plos One
|March 4, 2014
Summary
RNA CoMPASS is a new bioinformatics pipeline that analyzes both host transcriptomes and microbial metatranscriptomes simultaneously. This tool simplifies complex RNA sequencing data analysis for researchers, distinguishing cell types and identifying viral infections.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- High-throughput RNA sequencing (RNA-seq) is crucial for transcriptome analysis.
- Analyzing RNA-seq data for microbiome insights is an emerging area of interest.
- Existing bioinformatics tools often require command-line expertise, posing a challenge for many researchers.
Purpose of the Study:
- To present RNA CoMPASS, a comprehensive pipeline for simultaneous transcriptome and metatranscriptome analysis.
- To provide a user-friendly, web-based graphical interface for complex RNA-seq data analysis.
- To facilitate the analysis of large RNA-seq datasets using parallel computing.
Main Methods:
- RNA CoMPASS integrates existing bioinformatics tools and parallel computing.
- A web-based graphical user interface with intrinsic queuing manages the computational pipeline.
- The pipeline was evaluated using RNA-seq data from 45 B-cell samples, including lymphoblastoid cell lines (LCLs) and Burkitt's lymphomas (BLs).
Main Results:
- RNA CoMPASS successfully identified Epstein-Barr virus (EBV) in LCLs and a subset of BLs.
- Transcriptome analysis separated LCLs from BLs based on distinct phenotypes (blast-like vs. germinal center-like).
- Key signaling pathway differences were observed, including activated MYC signaling and reduced interferon and NF-kB signaling in BLs.
Conclusions:
- RNA CoMPASS demonstrates utility in simultaneous transcriptome and metatranscriptome analysis.
- The pipeline simplifies complex RNA-seq data analysis for biomedical researchers.
- RNA CoMPASS is freely available, promoting broader accessibility for scientific research.
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