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RNA-seq

RNA-seq

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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Author Spotlight: Exploring the Fermentation Microbiome Through Next-Generation Sequencing

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Pichia pastoris RNA-Sequencing and Data Analysis.

Julian Christopher Krappinger^1,2, Astrid Radkohl^3,4, Veronika Schusterbauer^5,6

¹Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria.

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

|October 1, 2025

Summary

This summary is machine-generated.

This study details RNA sequencing (RNA-seq) for transcriptome profiling, focusing on experimental design and data analysis. It provides a protocol for RNA extraction and guidance for yeast gene expression studies.

Keywords:

Data analysis Komagataella phaffii Pichia pastoris RNA extraction RNA-sequencing

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Expression of Recombinant Proteins in the Methylotrophic Yeast Pichia pastoris

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Published on: February 25, 2010

Area of Science:

Molecular Biology
Biotechnology
Bioinformatics

Background:

RNA sequencing (RNA-seq) is crucial for transcriptome profiling and comparing gene expression.
Understanding gene expression in microbes like Komagataella phaffii aids industrial process optimization.
A standard RNA-seq workflow involves experimental design, RNA extraction, library preparation, sequencing, and data analysis.

Purpose of the Study:

To provide a comprehensive protocol for RNA extraction.
To summarize key considerations for experimental design, library preparation, and sequencing.
To outline the fundamental steps in RNA-seq data analysis.

Main Methods:

Detailed protocol for RNA extraction.
Summary of best practices for experimental design, library preparation, and sequencing.
Step-by-step guide to RNA-seq data analysis, including quality control, alignment, quantification, and differential gene expression analysis.

Main Results:

A practical RNA extraction protocol is presented.
Critical aspects of experimental design and sequencing services are highlighted.
A clear data analysis workflow is described, covering essential bioinformatic steps.

Conclusions:

This work offers a valuable resource for researchers conducting RNA-seq experiments, particularly in yeast.
The protocol and guidance facilitate robust transcriptome profiling and gene expression analysis.
Effective implementation of RNA-seq workflows can enhance understanding and application of microbial biotechnology.