Services

Training

The Center’s Technical Director, Riccardo Racicot, is available to students, faculty, and staff, by appointment for training on any and all of the equipment in the CMB, and to help with experimental design, and consulting on how best to get the data you are looking for.  Please schedule an appointment on the CMB Scheduling Site at the link on the right side of this website or at cmb.scheduling.smith.edu

Sequencing

 

 

 

Click on the ‘Protocols’ page for info on how to set up a standard sequencing reaction using amplified DNA as template, from which you can modify to your needs (feel free to ask Riccardo for help with this).  This page also has some product recommendations. for sequencing set up and purification.

READ THIS FIRST!!

INSTRUCTIONS FOR SEQUENCING AND FRAGMENT ANALYSIS SERVICE REQUEST

Once you have performed and purified your sequencing reactions, we will run your purified sequencing samples using the Applied Biosystems 3500 Genetic Analyzer.  You need to follow the policies listed below to submit your samples and retrieve your data.

  1. The current cost for each ready-to-sequence sample is $1.50 for Smith labs and classrooms.  Unfortunately, we cannot offer these services to those outside the college. 
  2. Each Smith lab/class is responsible for purification of your DNA sequencing samples before submitting to the CMBS.
  3. Put PI initials plus sample’s serial number (must be 4 digits unless you’ve passed 9999, then use 5 digits) on the top of each tube such as “LAK0123”.
  4. Every time you submit a new batch of samples, the serial number of the sample must be sequential from the last batch.  Work out a system in your lab (sign out numbers) to ensure data does not get confused or overwritten.
  5. There are three boxes in the freezer (on the side wall) in Ford 123.  They are labeled as “Sequences To Be Run on 3100 Box 1” and “Box 2” and a third one that say Box 3 For Big Dye Xterminator Samples only.  Put samples in numerical order in the appropriate box.  If a group from your lab submits higher numbers than yours before you, and those tubes are still in the box when you get there, YOU MUSTrearrange tubes so that all fall in numerical order.  If a number is skipped, please leave a gap to call attention to this. Mis-numbered data is a very bad thing.
  6. Please fill out the Box 1 before you put into Box 2.
  7. Fill out the order form which is in the binder on the counter across from the freezer. Each lab has their own section.  Classes have a separate section as well.
  8. The CMBS will run sequencing samples on a “first come, first served” basis.
    We are using the ABI 3500 DNA Genetic Analyzer to run our sequencing samples.  Because 8 samples are injected to the capillaries simultaneously, it is better to try to submit several sequences at a time so we can try to fill all slots.  Samples will generally be loaded onto the machine after 11:30am every weekday.
  9. After samples have been run and sequence data have been extracted, the CMBS will transfer the data to a folder shared with you on Drive, usually by 9am the next business day if sequences are in before 11:30am.

Currently the CMBS does not have a second place to store your sequence data.  The sequence data will be trashed after a certain time (for now, it’s 3 months) in order to keep the sequencer functioning properly.  You are responsible for your data storage.

 

Fragment Analysis

We will run your post-PCR samples using the Applied Biosystems 3500 Genetic Analyzer. The current cost for each sample is $2.00 for Smith labs and classrooms.  Again, it may change in the future.  Please contact The CMB’s ITI, Riccardo Racicot, directly at rracicot@smith.edu if you plan to have fragment analysis samples.  When ready, the samples should be entered in the sequence order book just like sequences in the appropriate section pertaining to your class or lab.  Simply write “HID” with your sample serial numbers. Riccardo will run the samples for you and show you how to analyze the data and print a plot for each sample.  This print out will be your only product.   In general, a power point of the pdfs of the appropriate profiles is what is used for presentation to a class.