Gap genes are involved in segment determination during early development in dipteran insects
(flies, midges, and mosquitoes). We carried out a systematic quantitative comparative analysis
of the gap gene network across different dipteran species. Our work provides mechanistic
insights into the evolution of this pattern-forming network. As a central component of our project,
we created a high-resolution quantitative spatio-temporal data set of gap and maternal coordinate
gene expression in the blastoderm embryo of the non-drosophilid scuttle fly,
Megaselia abdita. Our data include expression patterns in both wild-type and RNAi-treated
embryos. The data—covering 10 genes, 10 time points, and over 1000 individual embryos—
consist of original embryo images, quantified expression profiles, extracted positions of
expression boundaries, and integrated expression patterns, plus metadata and intermediate
processing steps. These data provide a valuable resource for researchers interested in the
comparative study of gene regulatory networks and pattern formation, an essential step towards
a more quantitative and mechanistic understanding of developmental evolution.