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As we know, this platform is outdated and covers about 50%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.

Use of high-throuput sequencing approaches for problems in zebrafish biology

I would like to propose a workshop on the application of high-throughput sequencing technologies (i.e. 454, Solexa/Illumina, ABI) to problems in zebrafish biology. There are a wide variety of new possibilities that emerge with these high throughput sequencers that could be explored both as individual projects and community efforts. For example there is the Mouse Transcriptome Project done by Massively Parallel Signature Sequencing (MPSS) (see project here) that could be replicated in zebrafish using a platform superior to the one used for the mouse project. Possible uses for TILLING or cSNP detection, etc. could be discussed. Forum would be open to participants and possibly bringing in presentations from the main, commercially available, high-throughput sequencing platforms.

Shawn Burgess
Developmental Genomics Section
Genome Technology Branch
National Human Genome Research Institute
Bldg 50, Rm. 5537, MSC 8004
50 South Dr.
National Institutes of Health
Bethesda, MD 20892

ph: 301-594-8224
Fax: 301-496-0474
burgess@mail.nih.gov

http://genome.gov/staff/burgess

Morphogenesis workshop

I would like to propose a workshop on morphogenesis. I am particularly interested in early development/gastrulation but later evens such as organ morphogenesis could also be included. I envision both technical and conceptual aspects of morphogenesis being addressed. Possibilities include: in vivo vs. in vitro assays, methods/software/microscopy techniques, defining the open questions/burning issues in the field and how best to approach them.

Ashley Bruce
Assistant Professor
Department of Cell & Systems Biology
University of Toronto
25 Harbord Street, Room 615
Toronto, ON M5S 3G5