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Project-associated Open Datasets (primary and secondary)
For tertiary datasets (ones generated within the DevoWorm group), please visit DevoZoo
Caenorhabditis elegans primary:

Reproductive Capacity, Developmental Plasticity, and Evolution in C. elegans (B. Alicea). Archived at Figshare, doi:10.1101 /m9.figshare.045609. Referenced in: Alicea, B.  Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity in Caenorhabditis elegans (bioRxiv, doi:10.1101/045609).
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Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes) (B. Alicea). Archived at Figshare, doi:10.6084/ m9.figshare.2087719. Referenced in: Alicea, B.  Evolution in Eggs and Phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans (bioRxiv, doi:10.1101/042143)


Caenorhabditis elegans secondary:

Division Event (temporal) data. Original sources:
EPIC dataset - Murray, J.I. et.al Multidimensional regulation of gene expression in the C. elegans embryo. Genome Research, 22(7), 1282-1294 (2012).
Digital Development - Santella, A. et.al Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. Nucleic Acids Research, 44(D1), D781–D785 (2015).

Gene Expression data. Original sources: 
Murray, J.I.  et.al Multidimensional regulation of gene expression in the C. elegans embryo. Genome Research, 22, 1282-1294 (2012). WormBase.
Baugh, L.R. et.al The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo. Development, 132, 1843-1854 (2005). GEO accession number GSE2180.

Lineage Tree Database. Original source: 
Sulston, J.E., Schierenberg, E., White, J.G., and Thomson, J.N. The Embryonic Cell Lineage of the Nematode Caenorhabditis elegans. Developmental Biology, 100, 64-119 (1983).
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Positional Information data. Original sources: 
EPIC dataset - Murray, J.I. et.al Multidimensional regulation of gene expression in the C. elegans embryo. Genome Research, 22(7), 1282-1294 (2012)
WormGUIDES dataset - Bao, Z. Automated cell lineage tracing in Caenorhabditis elegans
. PNAS, 103(8), 2707-2712 (2006).


Ciona intestinalis secondary:


Division Event (temporal) and lineage data. Original sources:
Nishida, H. Cell lineage analysis in Ascidian embryos by intracellular injection of a tracer enzyme. III. Up to the tissue restricted stage. Developmental Biology, 121, 526–541 (1987).

ANISEED database - Tassy, O.et al. The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program. Genome Res. 2010, 20, 1459–1468.

Drosophila secondary:

Eye Imaginal Disc.
Wolff, T. Drosophila third instar eye disc. In: "The Development of Drosophila melanogaster". M. Bate and A. Martinez Arias eds. Cold Spring Harbor Laboratory Press, Plainview, New York (1993).


Whole Embryo (fused cells). Tomer et.al. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nature Methods, 9(7), 755-763 (2012).


Zebrafish secondary:

Whole Embryo (fused cells).
Keller et.al. Reconstruction of Zebrafish Early Embryonic Development by Light Sheet Microscopy. Science, 322 1065-1069 (2008).

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  • Home
  • Project Overview
    • Slack Channel
    • Project Roadmap
    • Education
    • Community Standards
  • People
  • Education, Notebooks, and Media
    • DevoLearn
    • DevoZoo
    • DevoWormML
    • Jupyter Notebooks
    • Media and Public Lectures
    • Google Summer of Code
  • Academic Output
    • Publications
    • Devoworm @ Github
    • Data Sources
    • Demos
  • Affiliations
    • OpenWorm Foundation
    • Orthogonal Research and Education Laboratory
  • Schedule/Join