SSBD:database

Key Organism Strain Cell Line Gene Symbol Protein name Protein tag Reporter Project ID Dataset ID Title Description Data Type Gene Ontology Biological Imaging Methods Method Summary Paper Information Medical Subject Headlines Person

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2-Kyoda-WormEmbryoRNAi

https://ssbd.riken.jp/database/2-Kyoda-WormEmbryoRNAi/

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ssbd-repos-000002

https://ssbd.riken.jp/repository/2/

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2013-09-02

2020-02-03

CC BY-SA

Image data, Quantitative data based on Experiment

373 ( Image datasets: 187, Quantitative data datasets: 186 )

1.6 TB ( Image datasets: 1.5 TB, Quantitative data datasets: 136.1 GB )

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Caenorhabditis elegans

B0336.10, B0361.10, B0464.7, C02F5.1, C02F5.9, C03C10.3, C05D11.11, C05D11.3, C07A9.2, C07A9.3, C16C10.6, C23G10.8, C26E6.4, C29E4.8, C29F9.7, C32A3.1, C34C12.8, C34E10.1, C34E10.2, C35D10.13, C38D4.3, C38D4.6, F01F1.7, F02A9.6, F10E9.8, F11H8.4, F20H11.3, F26F4.11, F35G12.8, F44B9.7, F54C8.3, F54E7.3, F56A8.6, F56D2.1, F58A4.3, F58B6.3, H38K22.2, K06H7.1, R07E5.14, R07E5.3, R08D7.1, R08D7.2, R08D7.3, R107.6, R10E11.8, R10E4.4, R12B2.4, R13F6.1, R144.2, T03F6.5, T07C4.7, T08A11.2, T10F2.1, T12D8.6, T12D8.7, T17E9.2, T20G5.1, T20G5.2, T20H4.3, T20H4.5, T23G5.1, T26A5.9, T26G10.1, W06F12.1, W07B3.2, Y111B2D.18, Y37D8A.14, Y43F4B.6, Y47D3A.29, Y49E10.14, Y49E10.19, Y66A7A.8, Y71H2AM.17, ani-1, baf-1, ccdc-55, cco-2, chc-1, cls-2, cpf-2, cts-1, cyk-1, dcn-1, ddx-23, dlc-1, eif-3.D, emb-30, gars-1, gei-4, glp-1, gop-2, gop-3, hcp-3, him-10, kbp-1, klp-19, knl-1, let-754, lis-1, lit-1, mcm-5, mdh-1, mdt-30, mel-28, mel-32, mev-1, nmt-1, pal-1, par-2, par-3, pars-1, pat-4, pbs-6, pcf-11, pie-1, rnp-4, rnr-1, rnr-2, rpb-2, rpb-8, rpl-23, rps-3, sas-4, sel-8, sms-4, snfc-5, taf-9, tag-170, tbx-33, tlk-1, tufm-1, ucr-1, ykt-6

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nuclear division dynamics

embryo development

nucleus

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XY: 0.105 micrometer/pixel, Z: 0.5 micrometer/slice

40 second for each time interval

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TimeLapse

DifferentInterferenceContrastMicroscope

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DIC

Leica DMRE

Hamamatsu Photonics ORCA C4742-95

Leica HCX PL Apo 100x/1.40 O

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Koji Kyoda, Eru Adachi, Eriko Masuda, Yoko Nagai, Yoko Suzuki, Taeko Oguro, Mitsuru Urai, Ryoko Arai, Mari Furukawa, Kumiko Shimada, Junko Kuramochi, Eriko Nagai, Shuichi Onami (2013) WDDD: Worm Developmental Dynamics Database., Nucleic acids research, Volume 41, Number Database issue, pp. D732-7

Published in 2013 Jan (Electronic publication in Nov. 20, 2012, midnight )

• doi: 10.1093/nar/gks1107
• pmid: 23172286
  

(Abstract) During animal development, cells undergo dynamic changes in position and gene expression. A collection of quantitative information about morphological dynamics under a wide variety of gene perturbations would provide a rich resource for understanding the molecular mechanisms of development. Here, we created a database, the Worm Developmental Dynamics Database (http://so.qbic.riken.jp/wddd/), which stores a collection of quantitative information about cell division dynamics in early Caenorhabditis elegans embryos with single genes silenced by RNA-mediated interference. The information contains the three-dimensional coordinate values of the outlines of nuclear regions and the dynamics of the outlines over time. The database provides free access to 50 sets of quantitative data for wild-type embryos and 136 sets of quantitative data for RNA-mediated interference embryos corresponding to 72 of the 97 essential embryonic genes on chromosome III. The database also provides sets of four-dimensional differential interference contrast microscopy images on which the quantitative data were based. The database will provide a novel opportunity for the development of computational methods to obtain fresh insights into the mechanisms of development. The quantitative information and microscopy images can be synchronously viewed through a web browser, which is designed for easy access by experimental biologists.

(MeSH Terms)

• Animals
• Caenorhabditis elegans/embryology[major]
• Caenorhabditis elegans/genetics[major]
• Cell Division/genetics
• Databases, Genetic[major]
• Genes, Helminth
• Internet
• RNA Interference

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Shuichi Onami , RIKEN , Quantitative Biology Center , Laboratory for Developmental Dynamics

Eru Adachi, Eriko Masuda, Yoko Nagai, Yoko Suzuki, Taeko Oguro, Koji Kyoda, Shuichi Onami

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