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Updated: Jul 17, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Adaptive sampling for nanopore direct RNA-sequencing.

Isabel S Naarmann-de Vries^1,2, Enio Gjerga^1,2, Catharina L A Gandor¹

¹Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany.

RNA (New York, N.Y.)

|September 6, 2023

Summary

This summary is machine-generated.

Adaptive sampling (AS) is now feasible for direct RNA sequencing (DRS), overcoming previous limitations. This method efficiently depletes unwanted RNA transcripts, improving the detection of low-abundance targets.

Keywords:

depletion direct RNA-seq enrichment heart mitochondria

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Last Updated: Jul 17, 2025

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Published on: June 3, 2019

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Nanopore long-read sequencing allows real-time control of individual nanopores.
Adaptive sampling (AS) enables targeted enrichment or depletion of specific DNA sequences during sequencing.
AS has not been previously applicable to direct RNA sequencing (DRS).

Purpose of the Study:

To establish the feasibility and utility of adaptive sampling for direct RNA sequencing.
To identify optimal parameters and characteristics for AS in DRS.
To demonstrate the application of AS for transcriptome-wide RNA analysis.

Main Methods:

Utilized a controlled in vitro transcript-based model system to test AS in DRS.
Evaluated the performance of depletion versus enrichment strategies for RNA.
Applied AS to poly(A)-enriched RNA samples from human and mouse tissues.
Characterized AS performance on complex transcriptome subsets, including Chromosome 11.

Main Results:

AS is feasible and effective for DRS, with depletion outperforming enrichment.
Depletion efficiency approached theoretical maximums in model systems.
Demonstrated efficient depletion (2.5- to 2.8-fold) of abundant mitochondrial transcripts in real-world samples.
Confirmed the general applicability of direct RNA AS across complex transcriptomes.

Conclusions:

Adaptive sampling is a valuable tool for direct RNA sequencing, addressing its unique challenges.
AS enhances the detection of lowly expressed transcripts by reducing the sequencing of highly abundant ones.
This approach significantly improves RNA sequencing efficiency and data quality.