Forcing 3700 to do wrapped runs in 384 well plates
Phillip San Miguel
pmiguel at purdue.edu
Tue Dec 14 08:48:39 EST 1999
I'm not sure if this is common knowledge among 3700
owners--but I didn't know until last week, so I'll presume
most of us don't know. If you use a 384 well plate on the
3700 it divides the plate into 4 quadrants and creates a run
for each quadrant. This is what one would expect. However,
its default quadrants are columns 1-6, 7-12, 13-18 and 19-24
instead of "wrapped" 96-well plate sectors. This may not
matter if you use formamide, but it creates a problem for
samples resuspended in water. With water-resuspened samples,
it is necessary to add extra water to the wells of samples
in the later runs to compensate for the evaporation before
they are loaded. Using a Hydra (or any standard 96-well
pipettor) to add extra water in columns 7-12 won't work. So
one must either use an 8 channel pipetor by hand or program
a Biomek (for example) to do it.
But there is a way around this. You can force the 3700
to load any way you would like. The 3700 collection
software automatically orders runs in the alphabetical order
of their run modules. To force the 3700 to load they way
you want: just make four copies your normal run module using
the "save as" option from the module creation wizard and put
alphabetical prefixes on the names. I used "A1, A2, B1, and
B2" as the prefixes. Then I made the plate record in
excel spreadsheet. I put the wells in wrapped quadrant order
. This makes it simple to assign the correct module to
each quadrant as a block in excel. Then I export the file as
a tab delimited text file with a ".plt" extension and
imported it into the data collection program as a plate
record. After I link the plate record I check the pane with
the list of runs that are scheduled by clicking on each run
and seeing that the 384 well icon produces the desired
"checker-board" blue and white pattern. It works fine.
Is it worth the trouble? Well it isn't much trouble
after you get it set up. And a 384 well plate costs less
than a 96 well PE plate. (Yes, that's right, per sample, the
96 well PE plate is more than four-fold the price of a 384
well plate.) So I think it is worth the trouble.
Phillip San Miguel
Purdue Genomics Center
By "wrapped" I mean the interleaved sectors A1, A2, B1
and B2. That is, the sectors as defined by a standard 8 x 12
(96-well) pin tool with 9 mm spacing.
Within the confines of "paired wells", of course--the
loading robot has two sample needles, with 18 mm spacing,
and it draws samples into both simultaneously and loads them
simultaneously. So, for example, wells A1 and A5 (of a 384
well plate) will always be in the same run. I don't know
anyway around that.
I didn't know this either, at first. It can be irritating
under certain circumstances. But as long as you know about
it, then it is a feature, not a bug.
By "prefix" I mean whatever you choose to type in front
of the module name.
I.e., A1-O23, A2-O24, B1-B23, B2-B24 -- I hope this is
making sense, if not I can go into more detail.
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