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RNA-Seq as a Tool to Study the Tumor Microenvironment.

Pudchalaluck Panichnantakul^1,2, Mathieu Bourgey², Alexandre Montpetit²

¹Department of Human Genetics, McGill University, Montreal, QC, Canada.

Methods in Molecular Biology (Clifton, N.J.)

|September 2, 2016

Summary

This study details RNA-Sequencing (RNA-Seq) methods for transcriptome analysis. RNA-Seq aids in understanding cellular function and disease, particularly cancer, by identifying abnormal gene expression.

Keywords:

Bioinformatics Next-generation sequencing RNA-Seq Tumor microenvironment

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Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

The transcriptome comprises various RNA molecules, reflecting cellular functional states and dynamics.
Transcriptome analysis is crucial for understanding biological processes and diseases like cancer.
Genomic studies increasingly rely on high-resolution transcriptome analysis to interpret genetic aberrations.

Purpose of the Study:

To describe RNA-Sequencing (RNA-Seq) experimental procedures.
To outline downstream data processing and analysis for RNA-Seq data.
To focus on identifying abnormally expressed transcripts and genes.

Main Methods:

RNA-Sequencing (RNA-Seq) for comprehensive transcriptome profiling.
Standardized experimental protocols for RNA sample preparation.
Bioinformatic pipelines for RNA-Seq data processing and analysis.

Main Results:

Detailed methodology for performing RNA-Seq.
Procedures for analyzing RNA-Seq data to identify expression patterns.
Focus on detecting aberrant transcript and gene expression levels.

Conclusions:

RNA-Seq provides high-resolution transcriptome analysis essential for biological research.
This methodology is key to understanding the functional impact of genomic changes in diseases such as cancer.
The described procedures facilitate the identification of molecular drivers in various biological contexts.