Integrating technologies for comparing 3D gene expression domains in the developing chick limb

Malcolm E. Fisher, Allyson K. Clelland, Andrew Bain, Richard A. Baldock, Paula Murphy, Helen Downie, Cheryll Tickle, Duncan R. Davidson, Richard A. Buckland

    Research output: Contribution to journalArticle

    39 Citations (Scopus)

    Abstract

    Chick embryos are good models for vertebrate development due to their accessibility and manipulability. Recent large increases in available genomic data from both whole genome sequencing and EST projects provide opportunities for identifying many new developmentally important chicken genes. Traditional methods of documenting when and where specific genes are expressed in embryos using whole amount and section in-situ hybridisation do not readily allow appreciation of 3-dimensional (3D) patterns of expression, but this can be accomplished by the recently developed microscopy technique, Optical Projection Tomography (OPT). Here we show that OPT data on the developing chick wing from different labs can be reliably integrated into a common database, that OPT is efficient in capturing 3D gene expression domains and that such domains can be meaningfully compared. Novel protocols are used to compare 3D expression domains of 7 genes known to be involved in chick wing development. This reveals previously unappreciated relationships and demonstrates the potential, using modern genomic resources, for building a large scale 3D atlas of gene expression. Such an atlas could be extended to include other types of data, such as fate maps, and the approach is also more generally applicable to embryos, organs and tissues.
    Original languageEnglish
    Pages (from-to)13-23
    Number of pages11
    JournalDevelopmental Biology
    Volume317
    Issue number1
    DOIs
    Publication statusPublished - 1 May 2008

    Fingerprint

    Optical Tomography
    Extremities
    Atlases
    Technology
    Gene Expression
    Embryonic Structures
    Genes
    Expressed Sequence Tags
    Chick Embryo
    In Situ Hybridization
    Vertebrates
    Microscopy
    Chickens
    Genome
    Databases

    Keywords

    • Animals
    • Chick Embryo
    • Databases as Topic
    • Extremities
    • Gene Expression Regulation, Developmental
    • Genomics
    • In Situ Hybridization
    • Technology
    • Tomography

    Cite this

    Fisher, M. E., Clelland, A. K., Bain, A., Baldock, R. A., Murphy, P., Downie, H., ... Buckland, R. A. (2008). Integrating technologies for comparing 3D gene expression domains in the developing chick limb. Developmental Biology, 317(1), 13-23. https://doi.org/10.1016/j.ydbio.2008.01.031
    Fisher, Malcolm E. ; Clelland, Allyson K. ; Bain, Andrew ; Baldock, Richard A. ; Murphy, Paula ; Downie, Helen ; Tickle, Cheryll ; Davidson, Duncan R. ; Buckland, Richard A. / Integrating technologies for comparing 3D gene expression domains in the developing chick limb. In: Developmental Biology. 2008 ; Vol. 317, No. 1. pp. 13-23.
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    Fisher, ME, Clelland, AK, Bain, A, Baldock, RA, Murphy, P, Downie, H, Tickle, C, Davidson, DR & Buckland, RA 2008, 'Integrating technologies for comparing 3D gene expression domains in the developing chick limb', Developmental Biology, vol. 317, no. 1, pp. 13-23. https://doi.org/10.1016/j.ydbio.2008.01.031

    Integrating technologies for comparing 3D gene expression domains in the developing chick limb. / Fisher, Malcolm E.; Clelland, Allyson K.; Bain, Andrew; Baldock, Richard A.; Murphy, Paula; Downie, Helen; Tickle, Cheryll; Davidson, Duncan R.; Buckland, Richard A.

    In: Developmental Biology, Vol. 317, No. 1, 01.05.2008, p. 13-23.

    Research output: Contribution to journalArticle

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