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High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM)

Flynn, C. J. and Sharma, T. and Ruffins, S. W. and Guerra, S. L. and Crowley, J. C. and Ettensohn, C. A. (2011) High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM). Developmental Biology, 357 (2). pp. 532-540. ISSN 0012-1606.

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The analysis of temporal and spatial patterns of gene expression is critically important for many kinds of developmental studies, including the construction of gene regulatory networks. Recently, multiplex, fluorescent, whole mount in situ hybridization (multiplex F-WMISH), applied in combination with confocal microscopy, has emerged as the method of choice for high-resolution, three-dimensional (3D) mapping of gene expression patterns in developing tissues. We have developed an image analysis tool, GeneExpressMap (GEM), that facilitates the rapid, 3D analysis of multiplex F-WMISH data at single-cell resolution. GEM assigns F-WMISH signal to individual cells based upon the proximity of cytoplasmic hybridization signal to cell nuclei. Here, we describe the features of GEM and, as a test of its utility, we use GEM to analyze patterns of regulatory gene expression in the non-skeletogenic mesoderm of the early sea urchin embryo. GEM greatly extends the power of multiplex F-WMISH for analyzing patterns of gene expression and is a valuable tool for gene network analysis and many other kinds of developmental studies.

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Additional Information:© 2011 Elsevier Inc. Received for publication 16 March 2011 Revised 20 June 2011. Accepted 22 June 2011. Available online 29 June 2011. The authors thank J. Rast for sharing unpublished information concerning the patterns of scl and gatac expression, J. Croce, D. McClay, and S. Ernst for providing plasmids, and B. McCauley and V. Hinman for providing F-WMISH images of starfish embryos. This work was supported by NSF Grant IOS-0745875 to C.A.E.
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Subject Keywords:Gene expression; Multiplex fluorescent in situ hybridization; Gene regulatory network; Sea urchin; GeneExpressMap; GEM; Image processing
Issue or Number:2
Record Number:CaltechAUTHORS:20111004-110505575
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Official Citation:C.J. Flynn, T. Sharma, S.W. Ruffins, S.L. Guerra, J.C. Crowley, C.A. Ettensohn, High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM), Developmental Biology, Volume 357, Issue 2, 15 September 2011, Pages 532-540, ISSN 0012-1606, 10.1016/j.ydbio.2011.06.033. (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:25559
Deposited By: Ruth Sustaita
Deposited On:04 Oct 2011 18:36
Last Modified:03 Oct 2019 03:07

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