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The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree

Nature Protocols volume 1, pages 1468–1476 (2006)Cite this article

Abstract

Lineage analysis of Caenorhabditis elegans is a powerful tool for characterizing developmental phenotypes and embryonic gene-expression patterns. We present a detailed protocol for the lineaging of embryos by computational analysis of 4D images of embryos that ubiquitously express histone–GFP (green fluorescent protein) fusion proteins through the 350 cell stage followed by manual editing. We describe how to optimize imaging settings for this purpose, the use of the lineage-extraction software, StarryNite, and the lineage-editing software, AceTree. In addition, we describe a useful polymer bead mounting technique for C. elegans embryos that has several advantages compared with the standard agar pad mounting technique. The protocol requires about 1 h of user time spread over 2 days to generate the raw lineage, and an additional 2 or 4 h to edit the lineage to the 194- or 350-cell stage, respectively.

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Figure 1: Screenshot of SNLauncher.
Figure 2
Figure 3: Examples of common lineage errors.
Figure 4: Lineage trees for the demo series 081505.

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References

  1. Sulston, J.E. & Horvitz, H.R. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110–156 (1977).

    Article  CAS  Google Scholar 

  2. Sulston, J.E., Schierenberg, E., White, J.G. & Thomson, J.N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119 (1983).

    Article  CAS  Google Scholar 

  3. Schnabel, R., Hutter, H., Moerman, D. & Schnabel, H. Assessing normal embryogenesis in Caenorhabditis elegans using a 4D microscope: variability of development and regional specification. Dev. Biol. 184, 234–265 (1997).

    Article  CAS  Google Scholar 

  4. Martinelli, S.D., Brown, C.G. & Durbin, R. Gene expression and development databases for C. elegans. Semin. Cell Dev. Biol. 8, 459–467 (1997).

    Article  CAS  Google Scholar 

  5. Bao, Z. et al. Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 103, 2707–2712 (2006).

    Article  CAS  Google Scholar 

  6. Boyle, T.J., Bao, Z., Murray, J.I., Araya, C.L. & Waterston, R.H. AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. BMC Bioinformatics 7, 275 (2006).

    Article  Google Scholar 

  7. Hope, I. A. (ed.) C. elegans A Practical Approach (Oxford University Press, Oxford, 1999).

  8. Boyd, L., Guo, S., Levitan, D., Stinchcomb, D.T. & Kemphues, K.J. PAR-2 is asymmetrically distributed and promotes association of P granules and PAR-1 with the cortex in C. elegans embryos. Development 122, 3075–3084 (1996).

    Article  CAS  Google Scholar 

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Acknowledgements

This research is partly funded by the US National Institutes of Health. J.I.M. is a fellow of the Jane Coffin Childs Memorial Fund for Medical Research. Z.B. is a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation.

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Authors and Affiliations

  1. Department of Genome Sciences, University of Washington Box 357730, Seattle, 98195, Washington, USA

    John Isaac Murray, Zhirong Bao, Thomas J Boyle & Robert H Waterston

Authors
  1. John Isaac Murray
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  2. Zhirong Bao
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  3. Thomas J Boyle
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  4. Robert H Waterston
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Corresponding author

Correspondence to Robert H Waterston.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Video 1

12 cell-stage image stack. Each frame is a separate image plane starting at the top of the stack. In addition to the 12 cells at this stage, the polar body is visible as a smaller, more intense region of staining. (MOV 19033 kb)

Supplementary Video 2

100 cell-stage image stack. (MOV 3467 kb)

Supplementary Video 3

200 cell-stage image stack. (MOV 2996 kb)

Supplementary Video 4

350 cell-stage image stack. (MOV 3111 kb)

Supplementary Video 5

Full image series at plane 15. Each frame is a separate time point, 1 min apart. The images are from plane 15, near the center of the embryo. (MOV 2980 kb)

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Murray, J., Bao, Z., Boyle, T. et al. The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nat Protoc 1, 1468–1476 (2006). https://doi.org/10.1038/nprot.2006.222

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