A new RNA sequencing approach: what is single cell transcriptomics?

An image to illustrate the concept of RNA sequencing and single cell transcriptomics
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Single cell transcriptomics is a next-generation RNA sequencing approach which allows a high-resolution view of cells.

Researchers from University of Southern Denmark, Wellcome Sanger Institute and BGI, published the study in the journal Genome Biology.

What is single cell transcriptomics?

RNA sequencing uses next-generation sequencing to analyse the presence of RNA in a sample.1,2

According to the University of Southern Denmark, single cell transcriptomics (i.e. scRNA-seq) is a next-generation sequencing approach that simultaneously measures the messenger RNA concentrations (encoded by DNA/genome/genetic blueprint) of thousands of genes, in individual cells.

This new approach allows a high-resolution view of cells to analyse heterogenous cell populations and individual cell functions.

Why is a new RNA sequencing approach desirable?

The University of Southern Denmark notes that although several single-cell protocols exist, the sequencing has traditionally been performed using Illumina technology and sequencing platforms.

The study authors compared traditional Illumina platforms to an alternative short-read sequencing platform for single cell transcriptomics, BGISEQ-500.

Dr Miaomiao Jiang, BGI’s co-lead author on the paper, explained: “The combination of higher throughput with marginally increased cost per lane makes the BGISEQ-500 an attractive alternative for scRNA-seq projects, where significant multiplexing is required alongside considerable read depth per cell.”

Mapping human cell types for health research

Jiang added: “This is the first study to compare Illumina HiSeq with BGISeq-500 sequencing platform for single-cell RNA-sequencing, offering researchers with an alternative sequencing option. Our study finds very similar performance in the compared metrics between the platforms. This would be extremely useful for large scale single-cell sequencing initiatives, generating reference maps of all human cell types and enhancing our understanding of human health.”

References

    1. Chu Y, Corey DR (August 2012). “RNA sequencing: platform selection, experimental design, and data interpretation”. Nucleic Acid Therapeutics. 22 (4): 271–4. doi:10.1089/nat.2012.0367.

2. Wang Z, Gerstein M, Snyder M (January 2009). “RNA-Seq: a revolutionary tool for transcriptomics”. Nature Reviews Genetics. 10 (1): 57–63. doi:10.1038/nrg2484. PMC 2949280. PMID 19015660.

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