High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development

High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development

Stefan C. Materna, Jongmin Nam and Eric H. Davidson

Gene Expression Patterns Article in Press, Accepted Manuscript doi:10.1016/j.gep.2010.04.002


Accurate measurements of transcript abundance are a prerequisite to understand gene activity in development. Using the NanoString nCounter, an RNA counting device, we measured the prevalence of 172 transcription factors and signaling molecules in early sea urchin development. These measurements show high fidelity over more than five orders of magnitude down to a few transcripts per embryo. Most of the genes included are locally restricted in their spatial expression, and contribute to the divergent regulatory states of cells in the developing embryo. In order to obtain high-resolution expression, profiles from fertilization to late gastrulation samples were collected at hourly intervals. The measured time courses agree well with, and substantially extend, prior relative abundance measurements obtained by quantitative PCR. High temporal resolution permits sequences of successively activated genes to be precisely delineated providing an ancillary tool for assembling maps of gene regulatory networks. The data are available via an interactive website for quick plotting of selected time courses. [non functional in Chrome Mac OS X edition – works in Firefox]

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