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I'm not sure how reliable the amplification procedure really is. Doing<br>
it twice might actually reduce your chances of finding the correct<br>
set of differentially expressed genes. <br>
<br>
Rohit<br>
<br>
<br>
Dapeng Cui wrote:<br>
<blockquote type="cite" cite="mids0ebbb1f.053@mailsrv21.gsu.edu">
<pre wrap="">My suggestion is to do microdissection and amplify both tissues starting
from the same amount of RNA/cells.
Dapeng Cui
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Stefano Calza <a class="moz-txt-link-rfc2396E" href="mailto:stecalza@tiscali.it"><stecalza@tiscali.it></a> 07/07/04 08:02AM >>>
</pre>
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</blockquote>
</blockquote>
<pre wrap=""><!---->Hi Rohit,
this was my point. But their (and mine at the statistical analysis
step) problem is that from the normal tissue itself they cannot collect
enough RNA. Then, what could be the best (or least bad)
solution?
Microdissection would bring into the normal sample a mixture of cells,
not only epithelial ones. Amplifying RNA from the normal tissue (they
already have the chips for th patholigical ones) would
probably bias the expression, though I guess the overall expression (or
also differentially at gene level?).
Summarizing: what could be the best procedure?
TIA,
Stefano
On Tue, Jul 06, 2004 at 08:18:13PM +0200, Ghai, Rohit wrote:
</pre>
<blockquote type="cite">
<pre wrap="">hi Stefan
I feel that such comparisons would not offer as much contrast
and clarity. Normal tissues would be best, even if isolation
is tedious. Cell lines grow in a completely different environment
than tissues. Gene expression is critically dependent on outside
cues from other cells in the tissue too. Of course, this also depends
</pre>
</blockquote>
<pre wrap=""><!---->on
</pre>
<blockquote type="cite">
<pre wrap="">what is the question you are asking. If its a question of
</pre>
</blockquote>
<pre wrap=""><!---->identifying
</pre>
<blockquote type="cite">
<pre wrap="">markers, these may be identified as one can then verify individual
</pre>
</blockquote>
<pre wrap=""><!---->markers
</pre>
<blockquote type="cite">
<pre wrap="">on a smaller scale. But for a better distinction of the processes
</pre>
</blockquote>
<pre wrap=""><!---->underlying
</pre>
<blockquote type="cite">
<pre wrap="">the disease state it would be better to use normal ovarian
</pre>
</blockquote>
<pre wrap=""><!---->epithelium.
</pre>
<blockquote type="cite">
<pre wrap="">regards
Rohit
------------------------------------------------------------------
Hi everybody.
This is definitely Off-Topic, but I'd like to have an opinion from
</pre>
</blockquote>
<pre wrap=""><!---->the many
</pre>
<blockquote type="cite">
<pre wrap="">biologist (but not only!) that populate the list, about the
</pre>
</blockquote>
<pre wrap=""><!---->following
</pre>
<blockquote type="cite">
<pre wrap="">problem:
A group of biologists is willing to study gene expression in ovarian
</pre>
</blockquote>
<pre wrap=""><!---->cancer
</pre>
<blockquote type="cite">
<pre wrap="">tissues relative to normal ones. As the normal ovarian epithelium is
</pre>
</blockquote>
<pre wrap=""><!---->single
</pre>
<blockquote type="cite">
<pre wrap="">layer, it's quite hard to get enough RNA. So
they are actually going to compare normal ovarian cell lines grown in
</pre>
</blockquote>
<pre wrap=""><!---->vitro
</pre>
<blockquote type="cite">
<pre wrap="">versus patological tissues. I feel a bit confused about this.
</pre>
</blockquote>
<pre wrap=""><!---->Wouldn't be
</pre>
<blockquote type="cite">
<pre wrap="">better to amplify the RNA from normal
tissues? Any other options?
Any insight will be very appreciated.
TIA,
Stefano
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<pre wrap=""><!---->
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