The temporal dynamics of the sea urchin regulome
Abstract
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/.
Additional Information
© 2022. Published by The Company of Biologists Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. I would like to thank Eric Davidson and Isabelle Peter for their tireless support. Johnathan Valencia and Enhu Li for the help in embryos collections. Julius Barsi for designing the Codeset and Maryam Ghaffary Saadat for developing the visualisation tool. Ezio Rosato, Alessandra Perugini and the Feuda lab for comments on the MS. This work is partially supported by a Royal Society University Research Fellowship (UF160226) and a Royal Society Research grant (RGF\EA\201005) to R.F. Author contributions. Conceptualization: R.F.; Methodology: R.F.; Software: R.F.; Validation: R.F.; Formal analysis: R.F.; Investigation: R.F.; Resources: R.F.; Data curation: R.F.; Writing - original draft: R.F.; Writing - review & editing: R.F.; Visualization: R.F.; Supervision: R.F.; Project administration: R.F.; Funding acquisition: R.F. The authors declare no competing or financial interests.Attached Files
Published - biolopen-11-059216.pdf
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biolopen-11-059216.pdf
Additional details
Identifiers
- PMCID
- PMC9493716
- Eprint ID
- 117021
- Resolver ID
- CaltechAUTHORS:20220916-665766000
Funding
- Royal Society
- UF160226
- Royal Society
- RGF\EA\201005
Dates
- Created
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2022-10-29Created from EPrint's datestamp field
- Updated
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2023-07-06Created from EPrint's last_modified field