Zebrafish Microarray Platforms

I would like to propose a workshop on zebrafish microarray
platforms. Microarray has been used to profile Gene
expressions for characterizing and studying genes that
control interesting biological phenotypes. We have primarily
been using Affymetrix Zebrafish Genome Array for studying
gene expression profiles in mutants and treated zebrafish.
As we know, this platform is outdated and covers about 50%
of zebrafish genes. We have worked with Sanger, UCSC, ZFIN,
and Nimblegen to design a next generation microarray chip
covering 37,177 transcripts including 12,694 alternative
transcript seqences. It is important to inform the community
about the strategies and tools we used to collect zebrafish
gene transcripts for the probe design and selection, the
informatic pipeline for analyzing data generated on this new
array, and results from experiments designed to access the
quality of the chip design. In addition, it is important to
discuss the gene annotation strategies that will expedite the
use of microarray technology. Agilent microarray platform is
used by the zf-model project in Europe. There are long-oligo
probes available from Compugen, MWG, and Operon for producing
spotted arrays. A cDNA platform has also been developed in
Singapore. This workshop will try to include information from
all platforms in presentations and discussions. Microarray
technology is complimentary to the next generation sequencing
technologies for analyzing gene transcription regulations,
which is a topic of the workshop titled as Use of High-
throughput Sequencing Approaches for Problems in Zebrafish
Biology.