Transcriptome Arrays:

Many Drosophila microarray groups started with the Drosophila Gene Collection cDNA set produced by the BDGP.  This collection represents approximately 40% of the predicted genes from the release 1 annotation.  Most of the groups now wish to move to whole transcriptome arrays and we believe that a high degree of consistency and data comparability can be achieved if everyone uses the same probe sets on their arrays.  It is our primary objective to try and generate a set of products that can be distributed to a several arraying centers throughout the world.

 

There are two possibilities for producing whole-transcriptome arrays in individual labs or facilities:

 

    Amplicons:  There are currently three sources of primer sets for generating PCR amplicons from genomic DNA, each set allows the production of relatively short amplimers (200-500bp).  The Heidelberg Set incorporates approximately 21,000 predicted ORFs from combined Celera and Sanger annotations.  Details of the platform are available at their web site http://hdflyarray.zmbh.uni-heidelberg.de/ and the primer set is available from Eurogentec http://www.eurogentec.be/ .  A second primer set , based on a design from Incyte Genomics, was generously donated by Incyte to Dr Brian Oliver for use by the Drosophila community.  These primers form the basis of the microarrays generated by the Drosophila Genomics Resource Center in Bloomington Indiana http://dgrc.cgb.indiana.edu and cover approximately 75% of the release 3.1 annotations.  A third set was designed by Dr. Kevin White in Yale http://genome.med.yale.edu/lab/default.htm and has been used by his group and in the Cambridge FlyChip facility http://www.flychip.org.uk .

 

    Long Oligo:  While there are clearly advantages to amplicon sets, the production of the large quantities of PCR product required to allow distribution of uniform sets to many laboratories is very challenging.  In light of this, there was a general consensus within the community that the production of a core probe set was best achieved by a large-scale synthesis of long oligonucleotides.  To this end, the INDAC consortium agreed to coordinate the design and production of a 70mer oligonucleotide set.  Oligos were designed according to release 4.1 of the genome annotation using a custom implementation of OligoArray2 http://berry.engin.umich.edu/oligoarray2/ developed by Dr David Kreil in the FlyChip group.  Synthesis of the set by Illumina http://www.illumina.com/  began in April 2005 and will be distributed during May 2005.  Labs in the consortium are listed here NETWORK.  Illumina will have sets derived from this original synthesis available for purchase.  An alternative supplier of a long oligo set that has bee used by several labs is Operon http://www.operon.com

 

The long term goal of INDAC is to ensure easy access to fully validated public domain array resources for the international Drosophila research community.