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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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Updated: May 10, 2025

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing

Published on: May 21, 2020

Automation of RNA-Seq Sample Preparation and Miniaturized Parallel Bioreactors Enable High-Throughput Differential

Karlis Blums¹, Josha Herzog¹, Jonathan Costa¹

¹Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany.

|April 26, 2025

Summary

This summary is machine-generated.

Automated at-line RNA-Seq in parallel bioreactors enables rapid transcriptome analysis for bioprocess development. This high-throughput method reveals molecular differences in yeast grown on various carbon sources, accelerating strain understanding.

Keywords:

RNA-Seq Saccharomyces cerevisiae automation gene expression high-throughput nanopore parallel stirred-tank bioreactors

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Published on: August 3, 2011

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Last Updated: May 10, 2025

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High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs

Published on: August 3, 2011

Area of Science:

Biotechnology
Molecular Biology
Systems Biology

Background:

Accelerating bioprocess development requires efficient, high-throughput experimental methods.
Automated systems, like liquid handling stations, are key to increasing experimental throughput.
At-line monitoring provides timely molecular data from bioreactor cultures.

Purpose of the Study:

To develop and validate an automated, at-line workflow for RNA-Sequencing (RNA-Seq) in parallel bioreactors.
To investigate the transcriptomic response of *Saccharomyces cerevisiae* to different carbon sources using high-throughput RNA-Seq.
To enable molecular-level understanding of microbial production strains during bioprocess development.

Main Methods:

Integration of 24 miniaturized bioreactors with a liquid handling station for automated sample preparation.
Development of an at-line workflow including enzymatic cell lysis, RNA extraction, and Nanopore cDNA library preparation.
Cultivation of *Saccharomyces cerevisiae* on six different carbon sources under controlled aerobic batch conditions.

Main Results:

Successful automated preparation of 24 cDNA libraries within 11.5 hours for Nanopore sequencing.
Differential gene expression analysis identified significant transcriptomic differences between glucose and pyruvate growth conditions (1383 genes).
Minimal transcriptomic changes were observed between glucose and fructose growth conditions (64 genes).

Conclusions:

The developed automated at-line RNA-Seq workflow is a powerful tool for high-throughput transcriptomic profiling of bioreactor cultures.
This approach provides valuable molecular insights into microbial responses to different substrates, aiding bioprocess optimization.
The method facilitates rapid understanding of microbial production strains at a molecular level.