You are here



Instrument Training

If you are not currently a user of CGC equipment, do not schedule a block of time on an instrument until you have read the training section, below


Scheduling a block of time to use a 3130XL or 3730 Genetic Analyzer, the BioRobot, or a PCR machine, is done using the online calendar. This allows users to see what is scheduled in the CGC for the next several weeks and where the openings are, from any networked computer.

General Scheduling Calendar Guidelines

You must include contact information in your calendar entry, a phone number and/or e-mail address.   To be fair to others and keep things running efficiently, please cancel reservations as soon as possible if your preparations don't work out.  Do not be late.  During busy periods we may have to follow a rule of passing time slots to other users if you are more than a 1/2 hour late and we haven't heard from you.  You can contact the lab director by phone at 206-616-0216 or by e-mail.


The 2 Day Rule CGC instrument users are expected to follow the 2 day rule when scheduling time on instruments.  According to the 2 day rule an individual user may not schedule a single continuous block of time on a particular instrument more than 48 hours long.  If no one has signed up for the next block of time after yours by the end of the 48 hours, then you may sign up for the next time block.  The exception to this rule is that you get "free weekend minutes".  Weekends are exempt from the rule, so it is possible to run something for up to 4 days as long as two of the days are Saturday and Sunday.



Scheduling Rules for the ABI 3130XL and 3730


These are the most heavily used instruments in the CGC and they have their own special scheduling rules.  Scheduling of an ABI Genetic Analyzer for DNA sequencing or fragment analysis should be done in appropriate size blocks of time for runs of 16 (3130XL) or 48 (3730) samples. The length of time required depends on the capillary length and polymer being used. A table of run times is available in a pop-up window linked on the online Scheduling Calendar welcome page.

The ABI 3730 loads plates from a stacker so plates can be added even while runs are in progress, which is not possible on the 3130XL platform. Most of the rules below will not apply to the 3730 because of the higher throughput and greater scheduling flexibility.


Maximum number of plates scheduled in advance - Any one user may only schedule 2 plates on 3130XL. Only after some of the plates are run can more be added to the calendar.



Full plate runs should be started late - Runs consisting of one or more full plates on The 3130XL should be started late in the afternoon, preferably 5 PM or later. This keeps days open for smaller runs, troubleshooting, etc., and makes more efficient use of the overnight hours.



Short notice cancellations - If a plate or run is cancelled on less than 4 hours notice and an alternate user of the time is not found, the user may be charged for one run, or $60.00 for 2 or more runs on 3130XL. Always send an e-mail to the cgc_users mailing list alerting people that a run or plate has been taken off the calendar less than 1 week in advance so that others can plan accordingly.



End times are fixed - So don't be late. The next user on the calendar after your runs can stop your runs to load theirs at their scheduled time. Contact the following users if you think you might be late to see if you can work something out. Otherwise you can cancel or adjust the number of runs to fit the remaining time.



Non-contiguous runs - If you are signing up for several runs on the same day, either do them back-to-back or allow enough time in between the runs for someone to reasonably be able to use it. That means a space of 3 or more hours on 3130XL.



Heavy Instrument Demand Periods - During times when the schedule becomes very tight we may invoke special rules to give scheduling priority to users in the Biology Department.  A “Heavy Demand” condition would be announced by the Lab Director on the cgc_users mail list and would remain in effect until the director announces that it is over. This will generally occur when the scheduling calendar for the 3130XL or 3730 is becoming filled 2 weeks or further in advance, but other factors  may be taken into account.  The heavy demand period rules can be found here.



cgc_users e-mail list
Laboratory users are required to subscribe to the cgc_users e-mail list in order to receive up-to-date notifications about equipment status, to facilitate things like finding partners to share a sequencing run with, or to ask the community of users for advice about something.  To subscribe to the cgc_users list go to: cgc_users list info and enter your e-mail address and name in the fields provided.


To subscribe to the cgc_users list go to:


MJ Research Dyad DNA Engine PCR machines
The CGC has two Dyad PCR machines, each of which has two alpha blocks which can hold either 96- or 384-well microplates. Users can program and operate the two alpha units independently, and the 384- and 96-well blocks can be mixed on one Dyad base unit. Thus, there are 4 separate calendar tracks for the PCR machines. However, the Dyad has to be switched off to swap alpha blocks, so you can not swap blocks if someone is already running a program on the other block.

Chromo4 Real Time PCR machine
A typical run for SYBR green reactions, which include a melting curve, takes about 3-3.5 hours.  Allowing for some time to set up, schedule 4 hours blocks of time.

Qiagen BioRobot 8000
When scheduling for use of the robot, allow yourself adequate time for set-up before the procedure runs, and for clean up afterwards. You will probably have to empty waste containers, fill water reservoirs, and you may have to mix up buffers for your Qiagen kit. The Turbo plasmid mini-prep and PCR clean-up protocols are fast, both done in about an hour for 96 samples, 4 hours for 4 plates of samples. The plant genomic DNA prep can take over 4 hours for one plate of samples. It all depends on how easy it is to grind your material on the Mixer Mill and how closely you follow the robot's progress. It is easy to make mistakes the first couple of times you do this. Allow 5 hours for a first time user doing plant DNA preps.

Computer Lab
Desktop PCs -The computer lab has two 32-bit Dell Optiplex 2.8 GHz PCs running Windows XP Professional, a Core2 Duo PC running XP Professional, and two Apple G5 1.8 GHz dual processor PowerMacs running OS X 10.5. 
Linux Workstation - There is a quad core HP xw8600 Workstation running 64-bit Ubuntu 10.04 where one can transfer files at high speed onto and off of the GenomicsServer from/to external hard drives (USB2/3, FW400, eSATA), run CLCBio GenomicsWorkbench, and run unix applications.

So far computer lab usage has not been heavy enough to need an online scheduling calendar. You can call before coming in if you need to know whether a machine is available or if you would like to reserve a time on one of the computers by sticky note on screen.

>>> Click Here To Open the Online Scheduling Calendar<<<

Training on CGC Equipment

ABI Genetic Analyzers
The automated equipment in the CGC is easy enough to use that training can usually be done using your first set of samples. Call or e-mail (preferred) the lab director (see below) to arrange a time to meet and go over the basics of the process and obtain some initial information about running cycle sequencing reactions and cleaning up the reaction products.


If you are going to be doing fragment analysis on a 3130XL or 3730, the operation of the machine is the same as for sequencing, but the software used is different. GeneMapper has a fairly steep learning curve, so you should set aside some time for working with a training CD before getting into your project in earnest. Call or e-mail the lab director to arrange a time to meet and go over the basics of the process, using the PCR machines, and using the training CD.



BioRobot and Apricot Plate Pipettor
For the BioRobot and Apricot there is more to learn about the machine and its operation.  There may also be things you need to be aware of to use a Qiagen kit for your particular purposes. Call or e-mail the lab director to arrange a time to meet and discuss your application, decide what preparations you will need to make, and get an overview of running a process on the Robot or Apricot. Then we can schedule a time for initial training and for a first sample run.


Error: Embedded data could not be displayed.

Date last changed Sep 29th, 2016 @ 09:22:32 PDT