ISH control

David Micklem dmicklem at
Fri Jun 19 21:02:03 EST 1998

In article <6mdpp1$si$1 at>, ELADER at AMBION.COM wrote:

>In article <Eus28w.2B4 at>,
>  rjv at (Richard Vernell) wrote:
>> My question is:
>> What is the best control for in situ hybridization with RNA probes.  Is an
>> irrelavent probe as valid as the sense probe?
>An unrelated sequence does not control for gc rich regions or repetitive
>sequences found in a specific probe. Go with the sense strand probe.

OK for GC rich I suppose (although any sequence of roughly equivalent
composition would surely do). But I don't understand why the sense strand
is a better control for repetitive sequences. To take one common simple
repetitive element in flies: CANCANCANCANCANetc. The anti-sense probe will
be etcN'TGN'TGN'TGN'TGN'TGN'TG which might hybe beautifully to the
gazzilion mRNAs containing CAN repeats and potentially mislead you about
the expression pattern of your-favourite-gene. The sense probe however
seems extremely unlikely to hybridise to this common repeat



D.R. Micklem,                            Time flies like an arrow... 
Beckman Institute,                   Fruit flies like a banana.       
Stanford, Ca 94305 USA           Email:dmicklem at
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