Discovering Biology in a Digital World

A few days ago, I wrote about a cool project that some high school students did where they used DNA sequencing to identify seafood.

One question that came up from one of my commenters was how a school would start a project like this. I'm totally biased, but I think DNA sequencing (well, actually the data analysis) is one of the most interesting things that a class can do as part of a research project. These days, getting started with this kind of project, wouldn't be so hard.

Here's are some ways that I would get started:

Find an existing project where my students could collaborate and get involved.




Scrape up the money to buy one of the new Bio-Rad kits.




Sequence DNA from an organism of your choice and send the samples to a sequencing service or the Joint Genome Institute. (They're sequencing DNA for free for educational projects.)




Skip the sequencing and work with the data.

How would these options work?
1. Find an existing project where my students could collaborate and get involved.

There are at least two projects (that I know of) where your school might be able to participate.

• A. The Howard Hughes Phage Hunter project: students are sequencing bacteriophage as part of a national project, funded by the Howard Hughes Medical Institute and the Department of Energy. I don't know what this costs, but I think it's all grant funded.


• B. Another is the National Geographic Genographic Project. In this project, students learn about their own DNA. Soldan International High School is one school that's involved in this work. You don't have to be a high school student to participate, this project is open to anyone who wants to be involved.

2. Use the Bio-Rad kit to clone and sequence GAPDH genes from plants. You can watch an on-line webinar and learn more about this. This path has the advantage that everything is packaged in a kit, you don't have to work out all the parts of the procedure from scratch.

3. Sequence an organism that you choose.

The advantage of working in a consortium is that you can use established procedures and maybe even get the lab supplies for free. The disadvantage is that you're restricted to working with organisms that someone else picked. You don't get to sequence the things that you choose, like seafood. So, what do you do? What do you do if you want to do your own thing?

Sequencing an organism of your choice is a bit more complicated, but not impossible. It's probably best, if you haven't done this before to go attend one the Phage Hunter classes or use a kit. Still, there are lots of steps that can be outsourced to commercial services, as long as you're not doing all the sequencing yourself, this is do-able.

If you want to sequence your own thing, here's an overview of the process:

• a. Decide what you want to learn from the experiment.
  

  Let's say you want to look at spinach in your grocery store. You would need to decide whether you want to sequence spinach DNA or DNA from the bacteria that are on that spinach.



• b. Decide which gene(s) or region of DNA you want to sequence.
  

  If you're sequencing bacteria, there are primers that you can use to amplify conserved regions of DNA. These regions are often used in experiments to identify bacteria. If you're sequencing a different organism, you can also use primers for ribosomal RNA genes, or you may want to do some research and find out what other people use.



• c. Figure out where you're going to get your DNA sequenced and learn how they want you to submit the samples. (I'll come back to this.)


• d. Find the primer sequences and order primers so that you can make lots of DNA from the piece you want to sequence.


• e. Use PCR to amplify the gene that you want to sequence.


• f. Send your DNA to the sequencing service.

How do you find a sequencing service?
Back to that sequencing service piece, the Joint Genome Institute in California has recently started a program where they will sequence DNA for free for educational projects. You can get more information about the JGI educational sequencing program here.

You can also look for core labs in your area. Many Universities have core facilities that sequence DNA for their researchers. Some of these facilities will also sequence DNA for outside groups. You can find many of them by searching Google with the phrase "DNA sequencing core facility" and adding your city or state. Many core labs post information about their pricing and sample requirements from their lab pages. I would find out what kinds of samples the facility handles, whether they want the samples in a 96 well plate, or a tubes, and what services they offer, before doing the experiment. You would also want to know what kind of information you'd get from the service. Would you be getting chromatograms or FASTA files? Would you get quality information or just base calls?

4. Skip the sequencing and work with the data.

I've been writing about this path quite a bit since this is what I do with my classes. You can search through this blog for topics, or put questions in the comments.