Workpackage 2: Analysis of expression patterns

Transgenic Expression in RetinaAnalysis of expression patterns is performed on a large scale by generating and imaging zebrafish transgenic for fluorescent proteins under the control of specific or endogenous enhancers (enhancer trap screening), as well as by in situ hybridization.

More than 5,000 transgenic founder fish expressing Green Fluorescent Protein (GFP) or Yellow Fluorescent Protein (YFP) under the control of zebrafish enhancer sequences are being screened, both to determine the spatial expression patterns of the corresponding genes, and to enable expression profiling in specific cell types (WP3). Most of this work is being performed at UiB, with the participation of a large number of researchers from inside and outside the consortium. UiB is also conducting research on new constructs to further enhance the efficiency of enhancer-trap screening. Moreover many project partners are generating GFP lines with specific enhancers.

The second focus is on the in situ hybridization analysis of 10,000 genes during embryogenesis. The majority of this work is being performed by CERBM. Due to the progress of the zebrafish genome project, the procedures for performing this aspect of the project have changed from using cDNA libraries as a source of genes for analysis to using gene predictions based upon Ensembl data, for which amplicons are provided to CERBM by Hubrecht Laboratory.

How to participate

External scientists are welcome to participate on a collaborative basis in the enhancer detection screen carried out at UiB. Please direct any request regarding this screen to Dr. Thomas Becker.

in situ analysis of ENSEMBL transcripts may be prioritized on request; please contact Dr. Christine Thisse.

Dissemination of results

The first batch of GFP expression patterns has been publicly released through the CLGY image database after publication as a refereed paper (Ellingsen et al., 2005). It is intended to make future batches directly available through this database.

in situ images and descriptions, using ZFIN-supplied ontologies, are directly released through
ZFIN. As of February 2006, the first 965 descriptions of in situ patterns have been released.