Lab guidelines

This lab primer is required reading for every new incoming student to the lab. And maybe even useful to read every once a year should you have settled here. It will help you to find your way around and to be quickly successful in the lab. Of course, most of the guidelines are also extremely important for keeping the lab functional and efficient for everyone else.

Words of wisdom for the graduate students:

  • Identify yourself with the project. It helps to be obsessive compulsive about your science, i.e. enjoying it.
  • M.S. graduate students will work towards one peer review first author publication. Ph.D. students better make it two and more...
  • Develop good scientific literature reading habits.
  • Stay organized. Good housekeeping habits are time and labor intensive but will save you lots of time in the long run, the latest when writing papers and your thesis.
  • No experiment without positive and negative control. Controls are a crucial part of experiments. There are two kinds of controls:
    • Positive controls usually test all standard reagents in an experiment and help to determine potentially false negative results. Positive controls often have the virtue of helping you to trouble shoot quicker when something did not work. 
    • Negative controls identify false positive results. This again can save big amounts of time by preventing you to continue further experiments with a product that is actually not what you think it is. So in either case, controls are not only important for evaluating final results, but for saving time to get there.
  • When you are in doubt about anything you are about to do, knock at my door at 3117 or drop me an email (friedrichm@wayne.edu).
Mentoring routines: 
At this point, we have one collective meeting per week together with the lab of Tiffany Cook at the Center for Molecular Genetics and Medicine on the third floor in Scott Hall, Medical Campus (http://www.genetics.wayne.edu/tiffany-cook). These meetings are either progress reports and  discussion of recent literature. In addition, there is a weekly 1:1 meeting with everyone to discuss ongoing progress. This is true for directed study students and graduate students.

Staying informed
If you are serious about research, you will need to conquer the literature meaning anything published of relevance for your topic. This means exploring the past but also staying informed about new publications. A highly recommended tool is pubcrawler:

http://pubcrawler.gen.tcd.ie/ 

Cleaning labware:

Everyone is responsible for cleaning glass and reusable plastic ware, and rinsing it with deionized water after experiments. No long term-storage in the sinks.

Setting up and documenting experiments:
We have a collection of protocols for all routine experiments in the lab. You can find this collection by going to the Stocks and Protocols site, which is implemented in Google Docs. You will also use Google Docs to create project specific digital lab notebooks. This has a number of advantages. You can start right away to use existing experimental protocol spreadsheets from our lab collection as templates to plan and document your own experiments. It will take you a while to learn this, but the time and labor saving aspects will soon become apparent as well. The protocols give you an outline of what to think about when setting up your experiments. You don't have to reinvent the wheel. At least not every wheel. Later on, the spreadsheets of completed experiments make consistent (and readable) documentation of your experiments. Also nice: Working in google docs automatically creates an off-site backup copy of all your data. It's safely in the cloud now. Last but not least, you and anyone with permissions can access your notebook from any place in the world, provided a somewhat decent computer and internet access. Or wireless phone for that matter.

Maintaining and updating lab protocols:
Our collection of lab protocols are only as useful as they are reliable and correct guides through experimental procedures. If you find a mistake or a problem, inform me about it. If the mistake is an easy fix, you can update the respective protocol yourself in our google Stocks and Protocols site. If you developed a new protocol, you will do everyone a great favor by adding it to the Stocks
and Protocols site.

Archiving protocols:
If you develop a new method, or successfully modify a method that is used in the lab, it would be of great help to add the protocol
 to the Stocks and Protocols site. This can be a great time saver for yourself, once you have to train a new student. Many protocols are immediately accessible for the students by just going online.

Archiving buffer recipes:
As with the protocols, if you prepare a complicated buffer, which we haven’t made before but is likely to be used often in the future, it would be of great help to add the information on buffer preparation to the worksheet “lablist_buffers” on the lab stock lists site. The buffer collection list is a little more advanced as it also includes math functions. Not sure how that works with google site spreadsheet functions. Only recommended for people who like to play.

Archiving oligos:
Every new oligo that is ordered/received by the lab needs to be entered in the oligo lab list on the 
lab stock lists site. The oligo will receive list number which should be written with sharpie on the lid of the tube. The oligos are stored in oligo stock boxes where they are sorted by number. This way, one reference number helps you finding reagent and information.

Using oligos:
When you start using an oligo, carefully take an aliquot from the stock solution that you predict to cover all the experiments you plan in the immediate future. Do not open the oligo stock tube for every experiment you need it for. That increases the risk of contaminating the stock. Work from your aliquot. If you need to be concerned to keep your aliquot contamination free, split your new aliquot into smaller ones and use them up one after the other.

Archiving antibodies:
Every new antibody that is received by the lab needs to be entered in the antibody lab list on the 
lab stock lists site. In many cases, we may also receive some documentation along with the antibody. This information is often very important. The info sheets are filed in the lab folder “Antibodies” where they are sorted and identified by the google sheet list number. So one reference number helps you finding reagent and information.

Using antibodies:
The required amount of antibody for a specific experiment can be taken directly from the stock as contamination is not such a big issue. However, everyone needs to be very conscientious in not leaving antibody exposed to room temperature for longer amounts of time.

Archiving plasmids:
Every new plasmid that we receive, and every new plasmid that you generate and contains sequence related to data likely to be published, or used in future experiments, needs to be entered in the plasmid lab list on the Google Docs labpage. Take time to complete the required info and description of the plasmid. A stock of the plasmid is stored in the plasmid boxes that are ordered according to list number. The number of the plasmid should be written well visible on the lid of the tube. The tube should be sealed off with parafilm. Alternatively, it is also OK to use screw top vials with seal for long-term storage. A description of the plasmid should be filed in the lab folder “Plasmids”.

Very important! Plasmid stocks NEVER run dry are ALWAYS returned. If the removal of your aliquot would deplete the stock, you first use stock plasmid to transform bacteria and make new stock. Then you take your aliquot and continue with experiments. This should be taken very seriously. Some stocks are hard if not impossible to replace.

Archiving digital images:
When you take and store digital images it is extremely important that you give every picture a name that serves as unique identifier and contains some basic information. Here is the highly recommended format:

First letter of genus and species name of the animal the image is from (Tc in the case of Tribolium castaneum), magnification used, date picture taken.

For example: Tc_20x_91207. This picture contains info on Tribolium at 20x taken on September the 12th in 2007.

Further, if it is likely that the image will be used in publication, a scale bar should be added to the image. That saves a lot of time later on.

Image files should be stored on your own computer, and as a back-up on the second hard drive connected to the MacMini of the Leica stereomiocroscope. The MacMini has also a DVD burner for generating backup DVDs. Be conscientious with backing up, and keeping you back-up files organized. It again is a big time safer in the long run.