Thanks for your help on microarrays
michael.lardelli at adelaide.edu.au
Tue May 15 09:39:38 EST 2001
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
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
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
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.
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!
Department of Molecular Biosciences
Discipline of Genetics and
Special Research Centre for the
Molecular Genetics of Development
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
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