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pubmed-article:21741377pubmed:dateCreated2011-8-30lld:pubmed
pubmed-article:21741377pubmed:abstractTextThe 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.lld:pubmed
pubmed-article:21741377pubmed:languageenglld:pubmed
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pubmed-article:21741377pubmed:statusMEDLINElld:pubmed
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pubmed-article:21741377pubmed:authorpubmed-author:SharmaTTlld:pubmed
pubmed-article:21741377pubmed:authorpubmed-author:CrowleyJ CJClld:pubmed
pubmed-article:21741377pubmed:authorpubmed-author:EttensohnC...lld:pubmed
pubmed-article:21741377pubmed:authorpubmed-author:FlynnC JCJlld:pubmed
pubmed-article:21741377pubmed:authorpubmed-author:RuffinsS WSWlld:pubmed
pubmed-article:21741377pubmed:authorpubmed-author:GuerraS LSLlld:pubmed
pubmed-article:21741377pubmed:copyrightInfoCopyright © 2011 Elsevier Inc. All rights reserved.lld:pubmed
pubmed-article:21741377pubmed:issnTypeElectroniclld:pubmed
pubmed-article:21741377pubmed:day15lld:pubmed
pubmed-article:21741377pubmed:volume357lld:pubmed
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pubmed-article:21741377pubmed:pagination532-40lld:pubmed
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pubmed-article:21741377pubmed:year2011lld:pubmed
pubmed-article:21741377pubmed:articleTitleHigh-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM).lld:pubmed
pubmed-article:21741377pubmed:affiliationDepartment of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.lld:pubmed
pubmed-article:21741377pubmed:publicationTypeJournal Articlelld:pubmed
pubmed-article:21741377pubmed:publicationTypeResearch Support, U.S. Gov't, Non-P.H.S.lld:pubmed