[BioC] CDF for GeneChip miRNA 2 array - Is there a miRNA 3 CDF?

[Steve Lianoglou]

Howdy,

On Fri, Nov 9, 2012 at 12:15 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
[snip]
> So I wonder if we are just doing something because we can't do what we
> really want to do, and doing nothing isn't an option. You can't get grants
> by sitting around waiting for the right technique to arrive, now can you?
[/snip]

The right thing has arrived: have your collaborator(s) do some CLIP
(HITS-CLIP/PAR-CLIP) against Ago2 in two conditions:

(1) Condition X
(2) Conditions X with your miRNA of interest somehow shut off (KO'd?
or  maybe w/ antisense LNA's to your miRNA(?))
(3) and likely coupled w/ some rna-seq in both conditions so you can
decouple differential ago binding from differential mRNA (target)
expression.

You can then work on more interesting problems that will arise in this
scenario, but at least you won't be guessing where your miRNA is
binding ... (sorry if that's not what we're talking about since I only
did a cursory scan of this thread ;-)

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact