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).
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).
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).
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).
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).
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).