[BioC] replication in continuous culture

[Peadar Ó Gaora]

Hello Bioconductorers,

I have a question regarding biological v technical replication in a
continuous culture model.  These are very expensive experiments to carry
out so are not normally repeated to get the usual biological replication
required.  So the following experimental design has been suggested.


 Cells are grown in a continuous culture fermenter and allowed to reach
stasis for 5 days.  At this point a sample (sample 1) is taken for
analysis.  Samples are taken on 2 more occasions at 3day intervals
(sample 2 and sample 3).  At the flow rate used, the cells present in
the tank should have been completely replaced in this time period.
 
 The conditions are then changed and samples taken as indicated above -
5d for stasis to be achieved followed by sampling after sufficient time
to allow for replacement of all cells (samples 4-6).
 
 
 We want to assess the effect of changed conditions (one only per
experiment) on gene expression using BioC/affy/LIMMA.
 
In the continuous culture model system, conditions are kept constant -
levels of nutrients, metabolites etc. so the environment for each set of
samples should (theoretically) be identical.
 
 My question is can we treat samples 1-3 as biological replicates and
samples 4-6 as biological replicates to compare with LIMMA?
 
 
 Any opinions much appreciated.
 

All the best,

Peadar
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Dr. Peadar Ó Gaora
UCD Conway Institute,
Belfield,
Dublin 4.

(01) 716-6915
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