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Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Overview of attention for article published in BMC Genomics, April 2017
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Title
Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos
Published in
BMC Genomics, April 2017
DOI 10.1186/s12864-017-3672-z
Pubmed ID
Authors

Han Rauwerda, Johanna F. B. Pagano, Wim C. de Leeuw, Wim Ensink, Ulrike Nehrdich, Mark de Jong, Martijs Jonker, Herman P. Spaink, Timo M. Breit

Abstract

Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage. On average one embryo per minute was analysed. The focus was on identification and description of the transcriptome dynamics of the expressed genes in this embryonic stage, rather than to biologically interpret profiles in cellular processes and pathways. In the late blastula to mid-gastrula stage, we found 6,734 genes being expressed with low variability and rather gradual changes. Ten types of dynamic behaviour were defined, such as genes with continuously increasing or decreasing expression, and all expressed genes were grouped into these types. Also, the exact expression starting and stopping points of several hundred genes during this developmental period could be pinpointed. Although the resolution of the experiment was so high, that we were able to clearly identify four known oscillating genes, no genes were observed with a peaking expression. Additionally, several genes showed expression at two or three distinct levels that strongly related to the spawn an embryo originated from. Our unique experimental set-up of whole-transcriptome analysis of 180 individual embryos, provided an unparalleled in-depth insight into the dynamics of early zebrafish embryogenesis. The existence of a tightly regulated embryonic transcriptome program, even between individuals from different spawns is shown. We have made the expression profile of all genes available for domain experts. The fact that we were able to separate the different spawns by their gene-expression variance over all expressed genes, underlines the importance of spawn specificity, as well as the unexpectedly tight gene-expression regulation in early zebrafish embryogenesis.

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Mendeley readers

The data shown below were compiled from readership statistics for 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 43 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 11 26%
Student > Ph. D. Student 8 19%
Student > Bachelor 6 14%
Other 4 9%
Student > Master 4 9%
Other 4 9%
Unknown 6 14%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 13 30%
Agricultural and Biological Sciences 12 28%
Environmental Science 2 5%
Unspecified 1 2%
Mathematics 1 2%
Other 4 9%
Unknown 10 23%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 April 2017.
All research outputs
#20,413,129
of 22,963,381 outputs
Outputs from BMC Genomics
#9,311
of 10,686 outputs
Outputs of similar age
#270,218
of 310,118 outputs
Outputs of similar age from BMC Genomics
#174
of 200 outputs
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