Quicker and Cheaper Single Cell RNA Sequencing Method Developed

Sequencing of RNA molecules

Austrian scientists have developed a quicker and less expensive method for RNA single-cell sequencing, which should help make large projects more feasible.

RNA sequencing is being used more and more to assess how genes are expressed within cells as it gives researchers more information than simply looking at genomic data. If this can be done for individual cells it is even more useful, for example, the heterogeneous nature of tumor tissue makes single cell analysis very helpful.

However, current single-cell RNA sequencing technology is very expensive and time consuming, which can make large-scale analyses difficult.

To make this kind of technology more accessible, Christoph Bock, Ph.D., principal investigator at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences and professor at the Medical University of Vienna, and team developed a new method called single-cell combinatorial fluidic indexing or scifi-RNA-seq.

Current methods for RNA single-cell sequencing are largely done using microfluidic droplet generators. These machines have many advantages, including the capacity for high throughput, relatively straightforward use and good data quality.

But they also have disadvantages. The cells are encapsulated into droplets and barcoded at this point. It is possible for more than one cell to be included in a droplet, meaning both would have the same barcode. Although this does not happen often, to avoid it the single cell suspension is fed into the machine slowly and at a low concentration, meaning costs are higher and the process is inefficient.

As described in the journal Nature Methods, to overcome this problem Bock and team managed to find a method to individually barcode different cells, before they are loaded onto a microfluidic chip meaning that more cells can be sequenced more quickly.

“On the popular 10x Genomics system, we use this method to measure 15 times more individual cells. The additional barcode also allows the user to mark and combine thousands of samples in advance, and to process those samples together in a single microfluidic analysis,” said Paul Datlinger, a researcher and graduate student in Bock’s lab as well as first author of the paper, in a press statement.

The researchers tested the scifi-RNA-seq system on various human and mouse cell lines and also by performing a multiplexed CRISPR screen in human T cells to assess T-cell receptor activation.

Bock thinks the method will be particularly useful for large scale projects that need to sequence a lot of cells, “scifi-RNA-seq enables efficient RNA sequencing for millions of individual cells, which facilitates the characterization of complex tissues, organs, and entire organisms… in biomedicine it is often useful to analyze many single cells, for example to discover rare stem cells in tumors or cancer cells in the blood.”

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