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

Luengo Hendriks, Cris L.; Keranen, Soile VE; Fowlkes, Charless C.; Simirenko, Lisa; Weber, Gunther H.; DePace, Angela H.; Henriquez, Clara; Kaszuba, David W.; Hamann, Bernd; Eisen, Michael B.; Malik, Jitendra; Sudar, Damir; Biggin, Mark D.; Knowles, David W.

doi:10.1186/gb-2006-7-12-r123

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

Journal Article · Wed Dec 20 23:00:00 EST 2006 · GenomeBiology.com

DOI:https://doi.org/10.1186/gb-2006-7-12-r123· OSTI ID:1626708

Luengo Hendriks, Cris L. ^[1]; Keranen, Soile VE ^[2]; Fowlkes, Charless C. ^[3]; Simirenko, Lisa ^[2]; Weber, Gunther H. ^[4]; DePace, Angela H. ^[2]; Henriquez, Clara ^[2]; Kaszuba, David W. ^[2]; Hamann, Bernd ^[4]; Eisen, Michael B. ^[2]; Malik, Jitendra ^[3]; Sudar, Damir ^[2]; Biggin, Mark D. ^[2]; Knowles, David W. ^[2]

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); DOE/OSTI
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
University of California, Berkeley, CA (United States)
University of California, Davis, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Academy of Finland; National Institute of General Medical Sciences (NIGMS); National Human Genome Research Institute (NHGRI)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626708

Journal Information:: GenomeBiology.com, Journal Name: GenomeBiology.com Journal Issue: 12 Vol. 7; ISSN 1465-6906

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
cellular resolution
orthographic projection
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Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline

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