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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: Oct 30, 2025

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq.

Martin Philpott^1,2, Jonathan Watson³, Anjan Thakurta^2,4,5

¹Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.

Nature Biotechnology

|July 2, 2021

Summary

We developed single-cell corrected long-read sequencing (scCOLOR-seq) for accurate error correction in single-cell sequencing. This method enhances analysis of gene expression and fusion transcripts from nanopore sequencing data.

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Area of Science:

Genomics
Molecular Biology
Biotechnology

Background:

Accurate sequencing of single cells is crucial for understanding cellular heterogeneity.
Existing long-read sequencing methods face challenges with error rates in molecular identifiers.
Novel methods are needed to improve the fidelity of single-cell transcriptomic data.

Purpose of the Study:

To introduce single-cell corrected long-read sequencing (scCOLOR-seq) for robust error correction.
To enable standalone cDNA nanopore sequencing of single cells with high accuracy.
To demonstrate the utility of scCOLOR-seq in various genomic applications.

Main Methods:

scCOLOR-seq utilizes dimeric nucleotide building blocks for synthesizing barcodes and unique molecular identifiers.
This approach allows for intrinsic error detection within oligonucleotide sequences.
The method enables standalone cDNA nanopore sequencing of single cells.

Main Results:

Demonstrated high barcode assignment accuracy using scCOLOR-seq.
Evaluated differential isoform usage in myeloma cell lines with improved precision.
Successfully detected fusion transcripts in a sarcoma cell line.

Conclusions:

scCOLOR-seq provides a powerful tool for accurate error correction in single-cell long-read sequencing.
The method significantly enhances the reliability of analyzing transcriptomic variations and detecting fusion events.
scCOLOR-seq opens new avenues for single-cell genomics research.