Microarray experiments with Drosophilas (miniscule amounts of RNA, cheap organisms)
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@paparountas-triantafyllos-2958
Last seen 9.9 years ago
Hi all, I would like to ask your expert opinions related to microarray experiments with Drosophilas. I have been asked to conduct a microarray experiment. According to the study design (pilot study) I need 2-4 groups : 1st->3rd treatments + 4th control. For each group 8-10animals would be ideal for the statistical power we want to achieve. (4 array groups - 8 arrays per group) If the experiment would be based on mice all that would be well as we need the brain nerve tissue, and we can get enough quantity of total RNA from mice brain. So one mice head goes into one microarray. But what happens with Drosophilas? Do you mix lets say 100 heads to get enough RNA? I believe pooling RNA would create technical replicates with no particular statistical value, and especially without a way to ascertain the biological validity of results.(100 mixed heads per 1 microarray, 8 microarrays per group= no clear way to understand which important gene is really overexpressed) I welcome your expert opinions. Kind regards, -- ----------------------------------------------------------------- Triantafyllos Paparountas - PhD+MSc Bioinformatics - BSc Molecular Medicine & Biochemistry - MSc Med. Statistics (Underway) http://www.bioinformatics.gr email: t_paparountas@bioinformatics.gr -------------------------------------------------------------- Affymetrix Microarray Analysis Expert -------------------------------------------------------------- [[alternative HTML version deleted]]
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@triantafillos-paparountas-4327
Last seen 9.9 years ago
Hi all, I would like to ask your expert opinions related to microarray experiments with Drosophilas. I have been asked to conduct a microarray experiment. According to the study design (pilot study) I need 2-4 groups : 1st->3rd treatments + 4th control. For each group 8-10animals would be ideal for the statistical power we want to achieve. (4 array groups - 8 arrays per group) If the experiment would be based on mice all that would be well as we need the brain nerve tissue, and we can get enough quantity of total RNA from mice brain. So one mice head goes into one microarray. But what happens with Drosophilas? Do you mix lets say 100 heads to get enough RNA? I believe pooling RNA would create technical replicates with no particular statistical value, and especially without a way to ascertain the biological validity of results.(100 mixed heads per 1 microarray, 8 microarrays per group= no clear way to understand which important gene is really overexpressed) I welcome your expert opinions. Kind regards, -- ----------------------------------------------------------------- Triantafyllos Paparountas - PhD+MSc Bioinformatics - BSc Molecular Medicine & Biochemistry - MSc Med. Statistics (Underway) http://www.bioinformatics.gr email: t_paparountas@bioinformatics.gr -------------------------------------------------------------- Affymetrix Microarray Analysis Expert -------------------------------------------------------------- [[alternative HTML version deleted]]
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Yes, is possible, have a look at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1599978/ Regards Yemi ________________________________ From: Triantafillos Paparountas <paparountas@fleming.gr> To: bioconductor@stat.math.ethz.ch Sent: Thu, October 28, 2010 6:42:58 PM Subject: [BioC] Microarray experiments with Drosophilas (miniscule amounts of RNA, cheap organisms) Hi all, I would like to ask your expert opinions related to microarray experiments with Drosophilas. I have been asked to conduct a microarray experiment. According to the study design (pilot study) I need 2-4 groups : 1st->3rd treatments + 4th control. For each group 8-10animals would be ideal for the statistical power we want to achieve. (4 array groups - 8 arrays per group) If the experiment would be based on mice all that would be well as we need the brain nerve tissue, and we can get enough quantity of total RNA from mice brain. So one mice head goes into one microarray. But what happens with Drosophilas? Do you mix lets say 100 heads to get enough RNA? I believe pooling RNA  would create technical replicates with no particular statistical value, and especially without a way to ascertain the biological validity of results.(100 mixed heads per 1 microarray, 8 microarrays per group= no clear way to understand which important gene is really overexpressed) I welcome your expert opinions. Kind regards, -- -----------------------------------------------------------------     Triantafyllos Paparountas     - PhD+MSc Bioinformatics     - BSc Molecular Medicine & Biochemistry     - MSc Med. Statistics (Underway)   http://www.bioinformatics.gr   email: t_paparountas@bioinformatics.gr --------------------------------------------------------------     Affymetrix Microarray Analysis Expert --------------------------------------------------------------     [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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It is possible to do this on a per-individual basis, but you will likely need at least one RNA amplification step. Locally, we have several honey bee researchers who have performed both array and RNA seq analyses using brain (specifically, mushroom bodies) from individual specimens, and using laser capture microdissection they have even isolated specific regions of individual brain. As mentioned at least one RNA amplification step is involved in these studies to generate enough RNA for analyses; experimental design and subsequent analyses take into consideration the caveats associated with that. Drosophila would be a bit more problematic (brain is ~ 1/5 the size of bee), but there should be enough literature to find some more answers on this. There is also FlyAtlas: http://130.209.54.32/atlas/atlas.cgi which may point to relevant publications for your needs. chris On Oct 28, 2010, at 12:42 PM, Triantafillos Paparountas wrote: > Hi all, > > I would like to ask your expert opinions related to microarray experiments > with Drosophilas. > > > I have been asked to conduct a microarray experiment. According to the study > design (pilot study) I need 2-4 groups : 1st->3rd treatments + 4th control. > For each group 8-10animals would be ideal for the statistical power we want > to achieve. (4 array groups - 8 arrays per group) > > If the experiment would be based on mice all that would be well as we need > the brain nerve tissue, and we can get enough quantity of total RNA from > mice brain. So one mice head goes into one microarray. > > But what happens with Drosophilas? Do you mix lets say 100 heads to get > enough RNA? I believe pooling RNA would create technical replicates with no > particular statistical value, and especially without a way to ascertain the > biological validity of results.(100 mixed heads per 1 microarray, 8 > microarrays per group= no clear way to understand which important gene is > really overexpressed) > > I welcome your expert opinions. > > Kind regards, > -- > ----------------------------------------------------------------- > Triantafyllos Paparountas > - PhD+MSc Bioinformatics > - BSc Molecular Medicine & Biochemistry > - MSc Med. Statistics (Underway) > http://www.bioinformatics.gr > email: t_paparountas at bioinformatics.gr > -------------------------------------------------------------- > Affymetrix Microarray Analysis Expert > -------------------------------------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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