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

Materna, Stefan C. and Nam, Jongmin and Davidson, Eric H. (2010) High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development. Gene Expression Patterns, 10 (4-5). pp. 177-184. ISSN 1567-133X. PMCID PMC2902461.

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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.

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Additional Information:© 2010 Elsevier B.V. Received 3 February 2010; revised 30 March 2010; accepted 6 April 2010. Available online 14 April 2010. The authors thank the NanoString team, and in particular Stephen Jackson and Sean Ferree, for their tireless support. Research was supported by NIH Grant HD 37105. Most of the funding for the purchase of the nCounter was a gift from the Ahmanson Research & Equipment Fund.
Funding AgencyGrant Number
Ahmanson FoundationUNSPECIFIED
Subject Keywords:Transcription factor; Gene expression time course; mRNA prevalence measurement; Embryogenesis
Issue or Number:4-5
PubMed Central ID:PMC2902461
Record Number:CaltechAUTHORS:20100624-110722230
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:18795
Deposited By: Tony Diaz
Deposited On:10 Jul 2010 04:17
Last Modified:03 Oct 2019 01:48

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