Worm Developmental Dynamics Database 2

Laboratory for Developmental Dynamics, Center for Biosystems Dynamics Research

Notice

Project

Our project aims to obtain a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos when each of all essential embryonic genes in all essential genes is silenced individually by RNA interference (RNAi).

The information is obtained by combining four-dimensional differential interference contrast (DIC) microscopy and computer image processing (Hamahashi et al. 2007). The information collection provides novel opportunities for developing quantitative and computational approaches towards understanding animal development.

References

• Yasuda, T., Bannai, H., Onami, S., Miyano, S., and Kitano, H. (1999).
  Towards Automatic Construction of Cell-Lineage of C. elegans from Nomarski DIC Microscope Images.
  Genome informatics. Workshop on Genome Informatics, 10, 144-154. PMID: 11072351
• Onami, S., Hamahashi, S., Nagasaki, M., Miyano, S., and Kitano, H. (2001).
  Automatic acquisition of cell lineage through 4D microscope and analysis of early C. elegans embryogenesis
  in Foundations of Systems Biology, H. Kitano, ed. (Cambridge, MA: MIT Press), pp.39-55.
• Hamahashi, S., Onami, S. and Kitano, H. (2005).
  Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking.
  BMC Bioinformatics 6, 125. DOI: 10.1186/1471-2105-6-125
• Hamahashi, S., Kitano, H. and Onami, S. (2007).
  A system for measuring cell division patterns of early Caenorhabditis elegans embryos by using image processing and object tracking.
  Syst. Comp. Jpn., 38: 12-24. DOI: 10.1002/scj.20783
• Kyoda, K., Adachi, E., Masuda, E., Nagai, Y., Suzuki, Y., Oguro, T., Urai, M., Arai, R., Furukawa, M., Shimada, K., Kuramochi, J., Nagai, E., & Onami, S. (2013).
  WDDD: Worm Developmental Dynamics Database.
  Nucleic acids research, 41(Database issue), D732-D737. PMID: 23172286, DOI: 10.1093/nar/gks1107
• Kyoda, K., Okada, H, Itoga, H. Onami, S. (2020).
  Deep Collection of Quantitative Nuclear Division Dynamics Data in RNAi-treated Caenorhabditis elegans Embryos
  bioRxiv 2020.10.04.325761; doi: 10.1101/2020.10.04.325761