Question: OT: cell lines and tissues
0
gravatar for Rohit Ghai
15.2 years ago by
Rohit Ghai80
Rohit Ghai80 wrote:
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 on what is the question you are asking. If its a question of identifying markers, these may be identified as one can then verify individual markers on a smaller scale. But for a better distinction of the processes underlying the disease state it would be better to use normal ovarian epithelium. regards Rohit ------------------------------------------------------------------ Hi everybody. This is definitely Off-Topic, but I'd like to have an opinion from the many biologist (but not only!) that populate the list, about the following problem: A group of biologists is willing to study gene expression in ovarian cancer tissues relative to normal ones. As the normal ovarian epithelium is single layer, it's quite hard to get enough RNA. So they are actually going to compare normal ovarian cell lines grown in vitro versus patological tissues. I feel a bit confused about this. Wouldn't be better to amplify the RNA from normal tissues? Any other options? Any insight will be very appreciated. TIA, Stefano
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ADD COMMENTlink modified 15.2 years ago by YUK FAI LEUNG140 • written 15.2 years ago by Rohit Ghai80
Answer: OT: cell lines and tissues
0
gravatar for stecalza@tiscali.it
15.2 years ago by
stecalza@tiscali.it290 wrote:
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: > 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 on > what is the question you are asking. If its a question of identifying > markers, these may be identified as one can then verify individual markers > on a smaller scale. But for a better distinction of the processes underlying > the disease state it would be better to use normal ovarian epithelium. > > regards > Rohit > > ------------------------------------------------------------------ > Hi everybody. > > This is definitely Off-Topic, but I'd like to have an opinion from the many > biologist (but not only!) that populate the list, about the following > problem: > > A group of biologists is willing to study gene expression in ovarian cancer > tissues relative to normal ones. As the normal ovarian epithelium is single > layer, it's quite hard to get enough RNA. So > > they are actually going to compare normal ovarian cell lines grown in vitro > versus patological tissues. I feel a bit confused about this. Wouldn't be > better to amplify the RNA from normal > > tissues? Any other options? > > Any insight will be very appreciated. > > TIA, > Stefano > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 15.2 years ago by stecalza@tiscali.it290
Answer: OT: cell lines and tissues
0
gravatar for Dapeng Cui
15.2 years ago by
Dapeng Cui40
Dapeng Cui40 wrote:
My suggestion is to do microdissection and amplify both tissues starting from the same amount of RNA/cells. Dapeng Cui >>> Stefano Calza <stecalza@tiscali.it> 07/07/04 08:02AM >>> 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: > 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 on > what is the question you are asking. If its a question of identifying > markers, these may be identified as one can then verify individual markers > on a smaller scale. But for a better distinction of the processes underlying > the disease state it would be better to use normal ovarian epithelium. > > regards > Rohit > > ------------------------------------------------------------------ > Hi everybody. > > This is definitely Off-Topic, but I'd like to have an opinion from the many > biologist (but not only!) that populate the list, about the following > problem: > > A group of biologists is willing to study gene expression in ovarian cancer > tissues relative to normal ones. As the normal ovarian epithelium is single > layer, it's quite hard to get enough RNA. So > > they are actually going to compare normal ovarian cell lines grown in vitro > versus patological tissues. I feel a bit confused about this. Wouldn't be > better to amplify the RNA from normal > > tissues? Any other options? > > Any insight will be very appreciated. > > TIA, > Stefano > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 15.2 years ago by Dapeng Cui40
Answer: OT: cell lines and tissues
0
gravatar for Rohit Ghai
15.2 years ago by
Rohit Ghai80
Rohit Ghai80 wrote:
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ADD COMMENTlink written 15.2 years ago by Rohit Ghai80
Hi. I want to use expresso to apply RMA with VSN normalization. I use the following code: expresso(dati,normalize.method="vsn",bgcorrect.method="rma",pmcorrect. method="pmonly",summary.method="medianpolish") Every is fine but when I get to ... ... normalizing...vsn: [skipped]: Error: L-BFGS-B needs finite values of fn What's wrong? TIA, Stefano
ADD REPLYlink written 15.2 years ago by stecalza@tiscali.it290
Answer: OT: cell lines and tissues
0
gravatar for YUK FAI LEUNG
15.2 years ago by
YUK FAI LEUNG140
YUK FAI LEUNG140 wrote:
Dear Stefano, Why don't you use both of them as controls? A group of RNAs from normal amplified RNA from tissue, and a group of RNAs from cell lines. Then you can make more comparisons! Best regards, Fai ------- Hi everybody. This is definitely Off-Topic, but I'd like to have an opinion from the many biologist (but not only!) that populate the list, about the following problem: A group of biologists is willing to study gene expression in ovarian cancer tissues relative to normal ones. As the normal ovarian epithelium is single layer, it's quite hard to get enough RNA. So they are actually going to compare normal ovarian cell lines grown in vitro versus patological tissues. I feel a bit confused about this. Wouldn't be better to amplify the RNA from normal tissues? Any other options? Any insight will be very appreciated. TIA, Stefano -- Yuk Fai Leung Department of Molecular and Cellular Biology Harvard University BL 2079, 16 Divinity Avenue Cambridge, MA 02138 Tel: 617-495-2599 Fax: 617-496-3321 email: yfleung@mcb.harvard.edu; yfleung@genomicshome.com URL: http://genomicshome.com
ADD COMMENTlink written 15.2 years ago by YUK FAI LEUNG140
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