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In this work, we used Nanostring N-counter technology, to evaluate the mRNA expression level of more than 330 regulatory genes over 34 time points covering the first three days of development of the sea urchin larvae. The hierarchical clustering of the mRNAs expression levels has identified groups corresponding to the major developmental landmarks (e.g. maternal to zygotic transition and gastrulation). Furthermore, comparison with previous experiments indicates high reproducibility of mRNA level temporal dynamics across batches. Finally, we generated an online tool to visualise gene expression during sea urchin larval development. The site can be accessed at and https://www621.lamp.le.ac.uk/nanostring_app/nanostring/.
Fig. 1. Principal component analysis of the temporal expression data. PCA analysis of Nanostring dataset from 0 to 72â hpf (n=2 replicates per time point). The 63.8% of variance is explained by the gene expression temporal dynamics.
Fig. 2. Heat map of gene expression. (A) Heat map of scaled expression for average mRNA expression level for 335 genes averages obtained from two replicates from 0 to 72â hpf (34-time points) of sea urchin larval development. The results indicate the existence of the X clusters that reflect the developmental transition during sea urchin embryonic development (lower part of the figure). (B) Developmental stages of S. purpuratus embryos at 15°C. Numbers indicate the six clusters identified.
Fig. 3. Reproducibility of mRNA measurements. Line plots obtained comparing mRNA expression from this work and those from Materna and collaborators (2010). The results indicate a high level of reproducibility of Nanostring measurements as well as of the transcriptional hierarchy.
Fig. 4. Snapshot of the expression data. The webpage allows for the visualisation of up to 100 genes simultaneously both using heatmap or line plot.
Geiss,
Direct multiplexed measurement of gene expression with color-coded probe pairs.
2008, Pubmed
Geiss,
Direct multiplexed measurement of gene expression with color-coded probe pairs.
2008,
Pubmed
Gildor,
Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin.
2016,
Pubmed
,
Echinobase
Howard-Ashby,
High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution.
2006,
Pubmed
,
Echinobase
Hu,
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors.
2019,
Pubmed
Huerta-Cepas,
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
2019,
Pubmed
Li,
Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo.
2014,
Pubmed
,
Echinobase
Materna,
High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development.
2010,
Pubmed
,
Echinobase
Metsalu,
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap.
2015,
Pubmed
Oliveri,
Global regulatory logic for specification of an embryonic cell lineage.
2008,
Pubmed
,
Echinobase
Peter,
A gene regulatory network controlling the embryonic specification of endoderm.
2011,
Pubmed
,
Echinobase
Tu,
Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus.
2014,
Pubmed
,
Echinobase
Waggott,
NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data.
2012,
Pubmed
