Gene Expression Database Parameters

Harry Mangalam mangalam at
Fri Jun 11 13:01:52 EST 1999

Hi All,

The background:
We (National Center for Genome Resources;, a nonprofit)
are designing an Internet-available gene expression database with a
Web browser front-end that will be stocked with expression data from a
wide source of biological systems and technologies (Affymetrix,
Synteni/Pat Brown slide arrays, Nylon blots, etc).  

We have the grand idea that this DB will have wide utility and browser
access to it will be freely available to all parties.  

The technology issues are relatively simple to deal with compared to
the biological compexities, hence this note.

We're still trying to design the underlying Database schema to be as
biologist-useful as possible and this of course is turning out to be
the hardest
part of it.  

I've taken responsibility for trying to address the parameters for the
single cell / tissue culture aspects of growth conditions, and since
this forum is probably the best in the world to post..

In order to assist with the design of this DB to make it as useful to
you, could you (or your cell culture guru) respond to the following

1) What are the growth conditions that you would be interested in
about for your experimental system?  some examples are:

NaCl mM                    
CaCl mM                    
KCl mM                     
glucose mM                 
glycerol %                 
PO4 mM
other ions?                     
// trace elements such as: 
Chromium ppM               
Strontium ppM              
Antibiotic mg/ml           
light photoperiod dark   
light photoperiod light  
light wavelength (nm)     
temperature C             
CO2 conc                 
N conc                   
O2 conc   
other gases?    
developmental state (and if so, how would you phrase the state?  
   Time in Days/Hours?, w/ a restricted vocabulary? (Stage2, 1st
   infection state
pathological conditions
2) What are the formal cell types that you deal with?  
3) What are the standard tissue culture media for your system?  
ie: Names of media such as YPY, L-broth, Eagle's, Dulbecco's
and if you have recipes for them (in electronic form, pointers to
online resources, or even paper copies that you'd be willing to fax or
scan), I'd be grateful.

4) What are the typical treatments that you use in your experiments?
   examples are: 
   transfection - what types?
   hormone/drug treatment
   temperature shock
   osmotic shock

5) If you have additional comments or queries about this project, I'd
be happy to try to answer them.  You can post to the group or directly
to me and I'll reply in the same manner.

Thanks in advance for any help you can give!


(Working off-site, hence the @home address).

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