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Related Experiment Video

Updated: May 10, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.

Wiep van der Toorn^1,2, Patrick Bohn³, Wang Liu-Wei^1,2,4

¹Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.

Nature Communications

|April 21, 2025

Summary

WarpDemuX offers fast, accurate adapter-barcoding and demultiplexing for nanopore direct RNA sequencing (dRNA-seq). This method enables cost-effective sample multiplexing, advancing transcriptomic research and viral diagnostics.

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Last Updated: May 10, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

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Published on: January 7, 2020

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

Nanopore direct RNA sequencing (dRNA-seq) provides valuable RNA biology insights.
Current dRNA-seq applications are hindered by limitations in accurate and cost-effective sample multiplexing.

Purpose of the Study:

Introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing method for dRNA-seq.
Enhance the speed, accuracy, and cost-effectiveness of dRNA-seq multiplexing.
Facilitate advanced (epi-) transcriptomic research and rapid phenotypic profiling.

Main Methods:

Developed WarpDemuX, an adapter-barcoding and demultiplexing approach for dRNA-seq.
Utilized fast raw nanopore signal processing and a lightweight machine-learning algorithm.
Designed optimized barcode sets for enhanced performance.
Integrated WarpDemuX with sequencing control software for real-time adaptive sampling.

Main Results:

Demonstrated WarpDemuX's utility in rapid phenotypic profiling of SARS-CoV-2 viruses using multiplexed sequencing.
Identified systematic differences in transcript abundance and poly(A) tail lengths during viral infection.
Showcased real-time enrichment of low-abundance viral RNA through barcode-specific adaptive sampling.

Conclusions:

WarpDemuX is a broadly applicable, high-performance, and economical multiplexing solution for dRNA-seq.
Enables advanced (epi-) transcriptomic research by overcoming current multiplexing limitations.
Facilitates rapid diagnostics and biological discovery through efficient sample processing.