Thanks for your help on microarrays

[Michael Lardelli]

Dear Zebrafish Community,

Thank you for your replies and support regarding interest in a 
microarray of zebrafish cDNAs. I have collated these replies and 
sent them to the funding body who might make a decision at the 
end of the month.  

If you are interested in microarrays but did not yet reply to my 
previous message then please send me your anticipated needs 
and I will pass these on - the more support we can show for this 
the better! To this end, I have included a copy of my original 
message at the bottom of this one. I would also like to answer 
some questions that were asked in the replies that I have received 
so far:  

1) Our immediate intention is to produce an array of cDNAs from 
embryos at 12 hours post fertilisation (@ 28.5C) and so it should 
include genes active in neurulation and somitogenesis. However, 
even if your work involves later or earlier stages of development the 
fact is that the array should represent approximately 10,000 genes 
(1/4? of the genome) and so should produce useful information for 
most applications.  

2) We have decided not to produce microarrays from those libraries 
for which sequencing has already been performed for the following 
reasons: A) The insert sizes are not necessarily optimal for PCR 
amplification - this seems to be the method of choice for DNA 
production for microarraying. Since our cDNA library is produced 
by a PCR-based method the clones are proven to be amplifiable. B) 
Apparently, there are relatively high levels of misidentification of 
clones in these libraries necessitating the resequencing of the 
clones in any case. C) The opportunity to produce a cDNA library 
from 5' ends gives information useful for morpholino expression 
knockdown experiments and promoter isolation. D) The 
presequenced/arrayed libraries must be purchased.  

3) Our intention is for the microarrays to be produced by The 
Australian Genome Research Facility. This national facility is 
experienced in production of microarrays (so quality should be 
high) and would also administer distribution of the microarrays and 
sequencing/distribution of clones of interest etc.  

4) If demand were high enough, I imagine that, once costs had 
been recovered, any further income from distribution of the 
microarrays could be put into furthering the sequencing of the 
10,000 clones.  

5) The timeline for all this? We have already produced the 
(normalized) library and are currently checking its level of 
redundancy. I believe that AGRF can move into production rapidly 
once funds are available.  

Once again, please send any additional messages indicating 
interest in this microarray as soon as possible. It is even more 
helpful if you can indicate how many copies you might want in the 
first year. Of course, there is NO obligation on your part to request 
the arrays if they are produced.  

Sincerely,

Michael Lardelli
___________________________________________________
ORIGINAL MESSAGE:
Dear Zebrafish community,

I need your help to assess the level of interest in the
zebrafish community for a microarray of zebrafish cDNAs.

For the past few months I have been negotiating with a couple of 
organizations in Australia for the production of a micorarray of 
10,000 zebrafish cDNAs. The array would be made from a 
normalized library of cDNAs corresponding to the 5' ends of 
transcripts. (The cDNAs are 0.5 - 1 kb in length and are produced  
by a novel method that we have developed.) Initially the identity of 
the clones on the array would be unknown but we will probably pay 
for up to 1000 of them to be sequenced ourselves and, if users 
identified interesting clones, they could ask to have them 
sequenced themselves. Anyway, just when everything seemed 
rosy and we appeared to have found support from a funding body to 
pay the Australian Genome Research Facility to make the 
microarray, the supporting fund changed its policy to one of cost 
recovery and now wants to know that it will eventually get its 
money back by sales of the microarrays!   

The only way to save the day is to see whether there is sufficient 
demand out there (internationally) to make the fund feel confident 
that it will eventually get its money back. What I need to know from 
you is whether, if the microarray described above were available, 
would you be interested in purchasing it and how many would you 
purchase per year?   

The microarrays would probably cost around Australian$200 each
to purchase (= US$100 each).

I am not looking for commitments, just expressions of probable 
interest. Please send your replies ASAP!  

Sincerely,

Michael Lardelli
___________________________________________________
Michael Lardelli
Department of Molecular Biosciences
Discipline of Genetics and
   Special Research Centre for the
   Molecular Genetics of Development
Adelaide University
5005
AUSTRALIA

Tel.    (Aust. = 61) (0)8 8303 3212  direct
        (Aust. = 61) (0)8 8303 5633  departmental secretary
Fax.    (Aust. = 61) (0)8 8303 4399
e-mail. michael.lardelli at adelaide.edu.au

Visit our UPDATED (!) website at:


http://www.science.adelaide.edu.au/genetics/lardelli/lardellilabwww.
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