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Using new sequencing technology to look at gene expression in a single cell

By dgmacarthur on April 7, 2009.

Jeffrey Perkel at Biotechnically Speaking has a great overview of a recent paper in Nature Methods (see also coverage at GenomeWeb).

The study in question used second-generation sequencing (with the ABI SOLiD system) to peer inside a single cell isolated from a mouse embryo. By sequencing the messenger RNA (mRNA) produced by the cell's genome they were able to generate a high-resolution snapshot of the genes switched on by the cell.

Isolating and analysing RNA from a single cell is no small technical feat, and although the technique still has its limitations - for instance, the technique can't detect certain RNA molecules (e.g. those without a poly(A) tail) and it's currently unable to discriminate which DNA strand the gene is expressed from - the results provide a far more comprehensive picture of gene expression than the array technology that has been the workhorse of gene expression studies for the last decade.

This is just a taste of the power of new sequencing technology to provide insight into fundamental biological questions. Here's Perkel:

I'm excited about the possibilities this study opens up. Here's one: from a single fertilized mouse egg, an entire body plan emerges. That body plan has anterior, posterial, dorsal, and ventral "sides," and it doesn't take long in development for those differences to become obvious. Wouldn't it be neat to study each cell at the two, four, eight, and sixteen cell stages, to see precisely when those changes, which initially are morphologically invisible, emerge?

The technique offers even greater potential for small organisms where development is very tightly constrained (e.g. the worm C. elegans): here it would now be possible to build a near-complete and quantitative catalogue of the genes switched on in every cell at each stage in development. This is very cool stuff.

Tags
transcriptome sequencing

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That is very cool. I was wondering who would take the next-gen there.

A project I'd love to see is wound repair gene expression--I think that would be amazingly informative.

I used to work at a company that had a proprietary database that contained many more splice variants and rare transcripts than people might expect. One set that I found very intriguing was the samples from emergency rooms.

As I write that I see it looks really morbid. But I still think it is a good project for that technology.