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Large-scale expression screening by automated whole-mount in situ hybridization


Burgtorf,  Carola
Max Planck Society;

Lehrach,  Hans
Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Quiring, R., Wittbrodt, B., Henrich, T., Ramialison, M., Burgtorf, C., Lehrach, H., et al. (2004). Large-scale expression screening by automated whole-mount in situ hybridization. Mechanisms of Development, 121(7-8), 971-976. doi:10.1016/j.mod.2004.03.031.

Gene expression profiling is an important component of functional genomics. We present a time and cost efficient high-throughput whole-mount in situ technique to perform a large-scale gene expression analysis in medaka fish (Oryzias latipes) embryos. Medaka is a model system ideally suited for the study of molecular genetics of vertebrate development. Random cDNA clones from an arrayed stage 20 medaka plasmid library were analyzed by whole-mount in situ hybridization on embryos of three representative stages of medaka development. cDNA inserts were colony PCR amplified in a 384-format. The PCR products were used to generate over 2000 antisense RNA digoxigenin probes in a high-throughput process. Whole-mount in situ hybridization was carried out in a robot and a broad range of expression patterns was observed. Partial cDNA sequences and expression patterns were documented with BLAST results, cluster analysis, images and descriptions, respectively; collectively this information was entered into a web-based database, ‘MEPD’ (, that is publicly accessible.