The Roslin Institute

Genetics and Genomics

ChickATLAS: a three-dimensional atlas of gene expression during chick development

The control of gene expression is important in embryonic development. Quantitative assays, such as microarrays, provide gene expression levels for large numbers of genes, but with low spatial resolution. In contrast, in situ methods, such as in situ hybridisation and immunohistochemistry, provide high spatial resolution, but poorer quantification and low genome coverage. Furthermore, crucial 3D data is lost with planar samples. Optical projection tomography (OPT) can capture the full 3D expression pattern in a whole embryo at a reasonably high resolution and at moderately high throughput.


A large database containing spatio-temporal patterns of expression for the mouse (EMAGE) has been created and is proving to be a valuable resource. Recently, the chick has become an important model for spatially and temporally controlled gain- and loss-of-function approaches.

To date, a well-established gene expression database for the chick does not exist. Thus, the aim of this project is to produce a 3D anatomical atlas and ontology of the chick embryo with a database of gene expression patterns during chick development. This database will be based on EMAGE and cross-referenced to the mouse through orthologous gene pairs ( Throughout this project, the data and framework will be used to identify groups of genes that are co-expressed in important signalling regions. Conservation of these genes will be examined in the chick and mouse.

This database will be made publicly available ( and will be a valuable resource to the developmental community.