Reducing laboratory costs

I was chatting with a colleague this morning about cutting lab costs. Rather than go into a lengthy discussion, I thought I would post a quick list of some things I do that bake a big difference in my lab budget.

- Use chemical methods when possible for DNA extractions rather than kits. Kits often cost $2-4 per sample. By chemical method in 2mL tubes, the cost immediately plummets. If you scale down your extraction into 96-well PCR plates, your reagent needs as well as your labor get minimized. Some of us just need a few PCR reactions. Depending on your organism, you may be able to do a rapid alkaline lysis method, further reducing your costs and material demands (e.g. http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CFsQFjAB&url=http%3A%2F%2Fwww.biotechniques.com%2Fmultimedia%2Farchive%2F00010%2F03344rr04_10933a.pdf&ei=98wQT7uZMam02gXiyIGECg&usg=AFQjCNF1HORNnYJQdbCmzbNYj-QGG0oJTw&sig2=lw4xwfnlpUgXNKVE3PPVrw).

- Reduce your PCR reaction volume. Most PCR kits suggest a reaction volume of at least 25uL, some as large as 100uL. I almost never do more than 10uL. If using a thermal cycler with adequate lid pressure, 6uL is possible in a 96 well plate. I now use 384-well plates and with the smaller wells (less headspace), I get good reactions of 4uL. That leaves me 2uL to run on a gel and another 2uL for capillary analysis. No waste!!

- Use reusable silicone PCR mats (e.g. http://www.phenixresearch.com/products/mpcs-3510-sealing-mat-pressure-fit-lid.asp). These things are great and I have always enjoyed less evaporation than with for instance, microseal B films. You can bleach or autoclave them if you like, but that will reduce their life. I simply throw used mats into a beaker with hot tap water for 10 minutes, rinse with RO water, and dry on a paper towel. I've never had a problem with my NTC reactions. For 384-well plates, try these: http://www.phenixresearch.com/products/smx-pcr384-sealing-mat.asp

- Use PCR plates (96 or 384) rather than strip tubes. Each plate costs about as much as 4 strip tubes last I checked. You don't have to throw out your PCR plate after running just a few reactions either. I keep partially used ones on my bench and just mark off the already used wells with a marker. When I need new wells, I peel back my silicone mat and use the unused wells, and don't bother to clean the mat until every well has been used. Still no problems with my NTCs.

- Agarose gels are reusable. Once or twice, but it can get pretty ugly. Make sure to keep spent gels intact in a sealed container (can hold numerous gels at once). Break the desired size of a gel into a flask for remelting and bring the mass back up where it should have been with RO water (if you had a 80mL gel, it should weigh ~80g). Add some new dye (e.g. ethidium or SYBR), pour, and run as always. You will notice some increased background, but for a quick gel to check some unimportant results, this works fine.

- SYBR safe can be used at 25,000X rather than 10,000X with no real loss of sensitivity.

- BigDye reactions (10uL) work fine with just 0.5uL BigDye. Add 2uL sequencing buffer, and sequence as before, or with this modified protocol I like: http://www.biotechniques.com/multimedia/archive/00003/BTN_A_000112499_O_3096a.pdf

Of course there are other things you can do, but this is all I have time for today...