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Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline

Cris L Luengo Hendriks1, Soile VE Keränen2, Charless C Fowlkes3, Lisa Simirenko2, Gunther H Weber4, Angela H DePace2, Clara Henriquez2, David W Kaszuba1, Bernd Hamann4, Michael B Eisen2, Jitendra Malik3, Damir Sudar1, Mark D Biggin2 and David W Knowles1*

Author affiliations

1 Berkeley Drosophila Transcription Network Project, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA

2 Berkeley Drosophila Transcription Network Project, Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA

3 Berkeley Drosophila Transcription Network Project, Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA

4 Berkeley Drosophila Transcription Network Project, Institute for Data Analysis and Visualization, University of California, Davis, CA 95616, USA

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Citation and License

Genome Biology 2006, 7:R123  doi:10.1186/gb-2006-7-12-r123

Published: 21 December 2006



To model and thoroughly understand animal transcription networks, it is essential to derive accurate spatial and temporal descriptions of developing gene expression patterns with cellular resolution.


Here we describe a suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology at cellular resolution in whole embryos. A database containing information derived from 1,282 embryos is released that describes the mRNA expression of 22 genes at multiple time points in the Drosophila blastoderm. We demonstrate that our methods are sufficiently accurate to detect previously undescribed features of morphology and gene expression. The cellular blastoderm is shown to have an intricate morphology of nuclear density patterns and apical/basal displacements that correlate with later well-known morphological features. Pair rule gene expression stripes, generally considered to specify patterning only along the anterior/posterior body axis, are shown to have complex changes in stripe location, stripe curvature, and expression level along the dorsal/ventral axis. Pair rule genes are also found to not always maintain the same register to each other.


The application of these quantitative methods to other developmental systems will likely reveal many other previously unknown features and provide a more rigorous understanding of developmental regulatory networks.