3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline
Cris Hendriks, Soile Keränen, Charless Fowlkes, Lisa Simirenko, Gunther Weber, Clara Henriquez, David Kaszuba, Bernd Hamann, Michael Eisen, Jitendra Malik, Damir Sudar, Mark Biggin, David Knowles
icon Background 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. Results 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. Conclusion 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.

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Cris Luengo Hendriks, Soile Keränen, Charless Fowlkes, Lisa Simirenko, Gunther Weber, Clara Henriquez, David Kaszuba, Bernd Hamann, Michael Eisen, Jitendra Malik, Damir Sudar, Mark Biggin, and David Knowles. 3d morphology and gene expression in the drosophila blastoderm at cellular resolution i: data acquisition pipeline. Genome Biology, 2006.

BibTeX Reference

    author = {Hendriks, Cris Luengo and Ker{\"a}nen, Soile and Fowlkes, Charless and Simirenko, Lisa and Weber, Gunther and Henriquez, Clara and Kaszuba, David and Hamann, Bernd and Eisen, Michael and Malik, Jitendra and Sudar, Damir and Biggin, Mark and Knowles, David},
    title = "3D Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline",
    journal = "Genome Biology",
    volume = "7:R123",
    year = "2006",
    tag = "biological_images"