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A database of Caenorhabditis elegans behavioral phenotypes

Nature Methods volume 10, pages 877–879 (2013)Cite this article

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Abstract

Using low-cost automated tracking microscopes, we have generated a behavioral database for 305 Caenorhabditis elegans strains, including 76 mutants with no previously described phenotype. The growing database currently consists of 9,203 short videos segmented to extract behavior and morphology features, and these videos and feature data are available online for further analysis. The database also includes summary statistics for 702 measures with statistical comparisons to wild-type controls so that phenotypes can be identified and understood by users.

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Figure 1: The Worm Tracker 2.0 (WT2) system and phenomic database ( http://wormbehavior.mrc-lmb.cam.ac.uk/ ).
Figure 2: Phenotypic summaries using selected features for subsets of strains.

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Acknowledgements

We thank C. Cronin and P. Sternberg for providing the code from their single-worm tracker, which serves as the basis for elements of our WT2 analysis GUI and phenotypic features cited from their publication; J. Lasenby and N. Kingsbury for guidance in computer vision; A. Deonarine for useful discussions; and R. Samworth, S. Chavali, G. Chalancon, S. Teichmann and M. Babu for guidance in statistics and bioinformatics techniques. This project was funded by grants to W.R.S. from the MRC (MC-A022-5PB91) and the National Institute on Drug Abuse, US National Institutes of Health (DA018341), a Gates Cambridge Scholarship (to E.Y.) and a long-term fellowship from the Human Frontier Science Program (to A.E.X.B.).

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Authors and Affiliations

  1. Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK

    Eviatar Yemini, Tadas Jucikas, Laura J Grundy, André E X Brown & William R Schafer

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  1. Eviatar Yemini
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  2. Tadas Jucikas
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  3. Laura J Grundy
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  4. André E X Brown
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  5. William R Schafer
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Contributions

E.Y. created the WT2 system (hardware and software), analyzed data and wrote the paper. T.J. developed the WT2 analysis pipeline and built the online database. L.J.G. conducted all experiments. A.E.X.B. analyzed data, supervised research and wrote the paper. W.R.S. designed experiments, supervised research and wrote the paper.

Corresponding authors

Correspondence to André E X Brown or William R Schafer.

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The authors declare no competing financial interests.

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Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Note (PDF 2058 kb)

Supplementary Table 1

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Supplementary Table 2

Supplementary Data Set (XLSX 45 kb)

Supplementary Table 3

Supplementary Data Set (XLSX 48 kb)

Supplementary Table 4

Supplementary Data Set (XLSX 42 kb)

Supplementary Table 5

Supplementary Data Set (XLSX 6853 kb)

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Yemini, E., Jucikas, T., Grundy, L. et al. A database of Caenorhabditis elegans behavioral phenotypes. Nat Methods 10, 877–879 (2013). https://doi.org/10.1038/nmeth.2560

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