Subtracted cDNA Probe

[Barbara]

I have two cell lines which are closely related and am attempting to
identify genes that aare expressed in one and not in the other.  I have a
cDNA library which is cloned into a lambda vector, and have screened
plaques twice with a subtracted probe.  In the past when I have tried this
technique I detected several false positives, but this time I really can't
find any hybridization that is above background levels.  I am debating
whether to try the hybridization again or to subclone the cDNA remaining
after subtraction (<10%).  My concern is that if the genes of interest are
not expressed very highly then they may be under-represented either in the
subtracted probe or in the phage library.  I would appreciate any
suggestions or past experiences that anyone may have.

Thank you,
Barbara