Scheduling and Training
Scheduling and Training to use Instruments in the CGC
Scheduling
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. 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 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.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.
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 or for a full plate of 96 samples. The length of time required depends on the capillary length and polymer being used.
A standard sequence run using the 50 cm
capillary array and POP7 polymer takes about 2 hours, and a fast run
takes about an hour on the 3730 (48 capillaries).
A long run on the 80cm array on the 3130XL (16 capillaries) in POP7 takes about 3 hours, and a short run about 2 hours.
Fragment analysis runs on the 3730 using a 50 cm array and POP7 take about 1 hour. Fragment analysis runs on 3130XL using the 80cm array for custom size standards can take over 3 hours.
Other custom run types have different durations. There is a table of run times available in a pop-up window on the online scheduling calendar. 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 wil 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, preferrably 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 will 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.
What
if you don't have a full run of 16/48 samples for an ABI Genetic Analyzer?
If you have fewer than 16/48 samples to run and you can be flexible about
when you analyze your samples, you can send a
note to the cgc_users mailing list a few days ahead of
time and try to find a partner to share the run with. Once you
find a partner you can reserve a time for the run on the online
calendar.
Of course, if time is money you can always run whatever number of
samples you want and your account will be charged the price of a full run.
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:
https://mailman.u.washington.edu/mailman/listinfo/cgc_users
and enter your e-mail address and name in the fields provided.
It is also important that other users can reach you for scheduling purposes. Samples on a second plate will begin processing after the current plate is finished. If a plate of samples is already processing, you can still enter another sample list into the plate manager and then a new run on a second plate can be placed in the queue by using the "pause" command, but only if done at the right time. NOTE: Consult Center staff before attempting this!
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
The computer lab has two Dell Optiplex 2.8 GHz PCs running Windows XP
Professional where users can work with the ABI software like Sequence
Analysis and GeneMapper in "offline" mode, DNA Workbench, etc.
These also
have the standard MS Office applications and the ability to back up
data on CDs (ROM and RW) and DVDs, and are networked. The
computer lab also has two Apple G5 1.8 GHz dual processor PowerMacs
running OS X 10.5. The ABI software doesn't run on Mac's, but you can
run Sequencher from the UW licenses, MacVector with Assembler, and DNA Workbench on them, use the MS Office apps,
run UNIX processes, do graphics, etc. The G5's also have CD/DVD
ROM/CD RW recorders, but not DVD burners.
At this point 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.
To open
the online
scheduling calendar >Click Here<
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.
