title: Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Berkeley Drosophila Transcription Network Project, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Cris L
authors.initials: CL
authors.lastname: Luengo Hendriks
authors.forename: Soile V E
authors.initials: SV
authors.lastname: Keränen
authors.forename: Charless C
authors.initials: CC
authors.lastname: Fowlkes
authors.forename: Lisa
authors.initials: L
authors.lastname: Simirenko
authors.forename: Gunther H
authors.initials: GH
authors.lastname: Weber
authors.forename: Angela H
authors.initials: AH
authors.lastname: DePace
authors.forename: Clara
authors.initials: C
authors.lastname: Henriquez
authors.forename: David W
authors.initials: DW
authors.lastname: Kaszuba
authors.forename: Bernd
authors.initials: B
authors.lastname: Hamann
authors.forename: Michael B
authors.initials: MB
authors.lastname: Eisen
authors.forename: Jitendra
authors.initials: J
authors.lastname: Malik
authors.forename: Damir
authors.initials: D
authors.lastname: Sudar
authors.forename: Mark D
authors.initials: MD
authors.lastname: Biggin
authors.forename: David W
authors.initials: DW
authors.lastname: Knowles
mesh_terms: D000818:Animals; D001483:Base Sequence; D001756:Blastoderm / Q000166:cytology*; D017931:DNA Primers; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics*; D005456:Fluorescent Dyes; D015870:Gene Expression; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D017931:DNA Primers; D005456:Fluorescent Dyes; D012333:RNA, Messenger