Posted on by Dr. Francis Collins
If you’re curious what innovations are coming out of the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, take a look at this video shot via a microscope. What at first glance looks like water dripping through pipes is actually a cool new technology for swiftly and efficiently analyzing the gene activity of thousands of individual cells. You might have to watch this video several times and use the pause button to catch all of the steps, but it provides a quick overview of how the Drop-seq microfluidic device works.
First, a nanoliter-sized droplet of lysis buffer containing a bead with a barcoded sequencing primer on its surface slides downward through the straight channel at the top of the screen. At the same time, fluid containing individual cells flows through the curved channels on either side of the bead-bearing channel—you can catch a fleeting glimpse of a tiny cell in the left-hand channel about 5 seconds into the video. The two streams (barcoded-bead primers and cells) feed into a single channel where they mix, pass through an oil flow, and get pinched off into oily drops. Most are empty, but some contain a bead or a cell—and a few contain both. At the point where the channel takes a hard left, these drops travel over a series of bumps that cause the cell to rupture and release its messenger RNA—an indicator of what genes are active in the cell. The mRNAs are captured by the primer on the bead from which, after the drops are broken, they can be transcribed, amplified, and sequenced to produce STAMPS (single-cell transcriptomes attached to microparticles). Because each bead contains its own unique barcode that enables swift identification of the transcriptomes of individual cells, this process can be done simultaneously on thousands of cells in a single reaction.