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Protocol for RNA in situ for specific splicing variants.

Teg Pipes teg at fruitfly.berkeley.edu
Mon Feb 16 07:48:55 EST 1998


akusano at STUDENTS.WISC.EDU (Ayumi Kusano) writes:

> My name is Ayumi Kusano.  I am a graduate student in Barry Ganetzky lab of
> Univ. of Wisconsin.  I am looking for protocol for RNA in situ
> hybridization for specific splicing variant.  If anybody knows any paper or
> protocol to detect expressed RNA which is spliced specifically, could you
> let me know about it?

If you have already cloned the splice variants you want to look at,
you could delete the parts of the cDNA that code for all variants 
and use the splice-form-specific bit to make your probe (just don't 
hydrolyze the shorter probe as long.)  

Also, making probes from introns using cloned genomic fragments works,
if an intron or 3'UTR is variant in the isoform you want to look at.  
Let the development reaction go longer and your intronic probe will
label nuclei (but not cytoplasm). 


						-Teg Pipes



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