This is  a slightly odd problem but I am hoping someone in the audience
has  encountered this.

 

I have a large library on shRNA's on about 350 96 well plates. Each well
has a unique shRNA. About 3 to 4 different shRNAs target a given gene
,but these 3-4  shRNA's can be anywhere in the 350 plates.  I would like
to reduce the size of the library by pooling shRNA's that target the
same gene. That is make a new pooled library , by picking from the
existing library (keeping the original library intact).

 

Constraints:

I have to use a robot, that can handle only 10 plates at a time. (one
(or more?) of the positions will have to be the used for plates I am
moving the genes to)

I can choose any 10 plates I like.

Say I only wanted to do this 10-plate-shuffle 20 times. Note robot moves
are REALLY SLOW !

 

What are the optimal 10 plate choices I can make to reduce the library
to the smallest number of plates (making shRNA gene specific pools)?

 

I was going to build a matrix of "gene- overlaps" on each plate and look
for best overlaps , recalculating after each pooling... then clean up
partial plates afterwards. Perhaps someone has some better optimization
algorithms or have done this already?

 

Thanks in advance

Paul 


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