ISH control

[David Micklem]

In article <6mdpp1$si$1 at nnrp1.dejanews.com>, ELADER at AMBION.COM wrote:

>In article <Eus28w.2B4 at riker.neoucom.edu>,
>  rjv at riker.neoucom.edu (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.
>
>Eric


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

YMMV,

David

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