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Deep Collection of Quantitative Nuclear Division Dynamics Data in RNAi-treated Caenorhabditis elegans Embryos

View ORCID ProfileKoji Kyoda, Hatsumi Okada, View ORCID ProfileHiroya Itoga, View ORCID ProfileShuichi Onami
doi: https://doi.org/10.1101/2020.10.04.325761
Koji Kyoda
1Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
2Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan
3Advanced Computational Sciences Department, RIKEN Advanced Science Institute, Yokohama 230-0045, Japan
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Hatsumi Okada
1Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
2Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan
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Hiroya Itoga
1Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
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Shuichi Onami
1Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
2Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan
3Advanced Computational Sciences Department, RIKEN Advanced Science Institute, Yokohama 230-0045, Japan
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  • For correspondence: sonami@riken.jp
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SUMMARY

Recent advances in bioimage informatics techniques have yielded quantitative data on multicellular dynamics from microscopy images of animal development. Several such data collections have been created for Caenorhabditis elegans embryos under various gene silencing conditions. However, because of the limited depth of the datasets, it is impractical to apply standard statistical methods to these collections. Here, we created a deep collection of quantitative data on nuclear division dynamics during the first three rounds of cell division in C. elegans embryos, in which 263 essential embryonic genes were silenced individually by RNA-mediated interference. The collection consists of datasets from 33 wild-type and 1142 RNAi-treated embryos, including five or more datasets for 189 genes. Application of a two-sample t-test identified 8660 reproducible RNAi-induced phenotypes for 421 phenotypic characters. Clustering analysis suggested 24 functional processes essential for early embryogenesis. Our collection is a rich resource for understanding animal development mechanisms.

In Brief Kyoda et al. used bioimage informatics techniques to create a deep collection of quantitative data on nuclear division dynamics in RNAi-treated C. elegans embryos for 263 essential embryonic genes. Statistical analysis identified 8660 reproducible RNAi phenotypes for 421 phenotypic characters. The collection is a rich resource for understanding animal development.

Highlights

  • Bioimage informatics quantified nuclear division dynamics in C. elegans embryos

  • From RNAi-silenced embryos we collected 1142 data sets on 263 essential genes

  • Statistical analysis identified 8660 reproducible RNAi phenotypes

  • Clustering analysis suggested 24 functional processes in C. elegans embryogenesis

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 05, 2020.
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Deep Collection of Quantitative Nuclear Division Dynamics Data in RNAi-treated Caenorhabditis elegans Embryos
Koji Kyoda, Hatsumi Okada, Hiroya Itoga, Shuichi Onami
bioRxiv 2020.10.04.325761; doi: https://doi.org/10.1101/2020.10.04.325761
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Deep Collection of Quantitative Nuclear Division Dynamics Data in RNAi-treated Caenorhabditis elegans Embryos
Koji Kyoda, Hatsumi Okada, Hiroya Itoga, Shuichi Onami
bioRxiv 2020.10.04.325761; doi: https://doi.org/10.1101/2020.10.04.325761

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