Grant proposal: next-gen sequencing prep equipment

If you are a graduate student interested in next-generation sequencing for your work, the Biology Department really needs your endorsement. We are applying for a University of Washington grant called the Student Technology Fee. This grant will provide us with state-of-the-art machines for next-generation library data generation.

How does this benefit you? Indeed, you will be trained and have access to some of the most cutting-edge instrumentation out there to generate some truly awesome Next Generation Sequencing (NGS) data, which will go right on your C.V. alongside the fact that you contributed to a successful grant proposal... something future employers and academic institutions will take notice of. But first we have to get the grant!

Here's where you fit in. I need one paragraph from each of you describing your status as a student/trainee at the University of Washington, the lab you work in, the research you're working on, and--most importantly--how you and your research will benefit from the suite of machines this grant will help us acquire, all of which are essential in generating NGS data, dontcha know. Now I know some of you probably have never used any of these fancy machines before, but that's the art of writing grant proposals:...requesting funding for things you haven't yet done but really, really want to do. Below, I wrote a quick summary of each machine and how it facilitates NGS library preps. Follow the links for more information or just ask me because I've done it all.

For examples, please see the STFC proposals page. I need all these back before Thursday (1-10-13) otherwise I can't guarantee you'll be on the grant.

We're applying for these instruments:

1. The Blue Pippin is a programmable automatic DNA size selector. Each library prep for NGS has a dreaded step near the end where you run your entire sample on a gel and visually try to cut out a tiny band that contains all the DNA you'll be sequencing. Slicing up agarose gels with razor blades is an inexact science. The Blue Pippin takes out much of the guesswork. You simply load your sample into a chamber and tell the machine the DNA size you desire and walk away. Half hour later you have your cleaned, size-selected sample ready to go.

2. A Qubit is like a nanodrop but is far more accurate. NGS library preps are demanding protocols and we need to know exactly how much DNA we're starting with. THe Qubit is the industry standard for this job. Unlike a nanodrop its reagents are highly biased to double-stranded DNA nucleotides, leaving all the RNA and single stranded DNA behind. This instrument is an essential part of any NGS library prep pipeline. It's a must-have.

3. Bioanalyzer [pdf]. Another must-have for the NGS library prep pipeline. After you finish the library prep, and before you sequence your samples, you must validate that you have DNA to be sequenced and that it's the correct size. The only way to do this is with the bioanalyzer. Most sequencing facilities will not touch your sample without this data.

4. Bioruptor. We call this mechanical DNA shearing. Genomic DNA is very long, too long to sequence. Before we start our library prep we need to chop up the DNA into a uniform size of small sequenchable fragments. The most tried-and-true method for doing this is through mechanical shearing using a bioruptor. Other technologies are either cost prohibitive or are too unpredictable in their shearing.

5. Apple iMac. The Biodiversity Genomics Laboratory located in Kincaid Hall, 5th floor has a computer laboratory space for NGS analysis. This computer will have a software that will be able to clean and sort your millions of reads of sequence data. It will also be able to do de novo assemblies of whole genome sequencing, sequence alignment and BLAST search your sequence to existing genomic libraries. The software is already available, we just need a machine to run it on.

Sample student endorsements can be found at http://techfee.washington.edu/proposals/.

-- Tony Gill, Leache Lab

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