384s on 3700s

Paul Shinn pshinn at mail2.sas.upenn.edu
Mon Feb 7 18:12:15 EST 2000

   I am beginning to venture into the 384 realm after the POP5 install. 
My first 384 test plate ran absolutely above expectations.  The cycle
sequencing was done in a 384 well plate made by Robbins.  The diagonal
plate notches are on the "right" side of the 384 unlike the PE 384.  A
little "modification" of the 3700 base plate took care of that.  Our
1/8th and 1/6th terminator reactions are 9ul in volume so I added 40ul
75% isopropanol to the 384.  That brings the volume right below the top
of the well.  I then sealed it with foil, flipped it once, let it sit 20
minutes at RT, spun at 3000rpm (RT) in a plate spinner for 20 minutes,
invert spin until 1200 rpm, and dry.  I only had reactions in quadrant 4
of the plate just to be safe but if one quadrant worked, I don't see why
the others wouldn't.  The 3700 picked up sample from the same plate
cycling was done.  We usually move our 384 to 4 96s.  Time and money
   Since we use a Hydra 96 to add the DNA to the plate, my sample sheet
was staggered as suggested by Phillip San Miguel.  Making a sample sheet 
for only one quadrant wasn't too bad, but I couldn't imagine doing it in 
Excel each time.......so I wrote a perl script.  I will make it 
available here for anyone interested.  You will want to change some of 
the parameters to suit your own setup, of course.  Each of our 96 well 
plates is labeled as so:

123M45x  -where "123" is a project #--always 3 digits for us
         -"M" is just a delimiter between the project and plate, but 
           since we use M13, that's what I think of it as
         -"45" is the plate number of the project
         -"x" is dye terminator chemistry.  I don't plan on running 384 
          dye primers just yet

The script will take 4 plate names of this format and make a sample 
sheet where the first 96 are quadrant one (A1, plate1), the second 96 is 
quadrant two (A2, plate2), and so on.  It will also fill in the 
"project" slot and the Run modules and analysis modules for each plate.
It's really not all that complicated of a script and it could probably 
be streamlined, but I'm just starting with perl so be kind :)  Script is 
at the bottom.  Please tell me if you find any errors.  I haven't 
actually used the sample sheet yet but the output looks about right.


Paul Shinn    
Sequencing Coordinator                                    ,___o
pshinn at neomorph.bio.upenn.edu                            _-\_<,
Arabidopsis thaliana Genome Center                      (*)/'(*)
(215) 573-7256

#Paul Shinn
#pshinn at neomorph.bio.upenn.edu

#proper plate format is 123M45X   where "123" is the project "45" is the plate
#script syntax:
#		384sheet plate1 plate2 plate3 plate4
#output is plate1.plt

($first, $second, $third, $fourth) = @ARGV;

@quad_1_3_column=(1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23);
@quad_2_4_column=(2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24);

open SHEET, ">$first.plt" or die "Couldn't create $first.plt!\n";
print SHEET "1\n";
print SHEET "$first\tSQ\t384-Well\tatgc\n";
print SHEET "Well\tSample Name\tDye Set\tMobility File\tComment\tProject Name\t";
print SHEET "Sample Tracking Id\tRun Module\tAnalysis Module\n";

#first quadrant of 384
$project=$array[0]; $plate=$array[1]; $chemistry=$array[2];

#second quadrant of 384
$project=$array[0]; $plate=$array[1]; $chemistry=$array[2];

#third quadrant of 384
$project=$array[0]; $plate=$array[1]; $chemistry=$array[2];

#fourth quadrant of 384
$project=$array[0]; $plate=$array[1]; $chemistry=$array[2];

close SHEET;

sub arrange384 {
   for ($column=0; $column<@quad_column; $column++) {
      for ($row=0; $row<@quad_row; $row++) {
          print SHEET $quad_row[$row].$quad_column[$column]."\t";
          print SHEET $project."M".$plate.$platerow[$row].($column+1)."\.".$chemistry."\t";
          print SHEET "E\tBD_lowT\.mob\t\t$project\t\t$module\tLowT\.saz\n"

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