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Series GSE50548 Query DataSets for GSE50548
Status Public on Dec 11, 2014
Title Spatiotemporal embryonic transcriptomics reveals the evolutionary history of the endoderm germ layer
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary The concept of germ layers has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years. Of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla Cnidaria and Ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve. The origin of the ectoderm and endoderm germ layers, however, remains unclear, with models supporting the antecedence of each as well as a simultaneous origin. Here we determine the temporal and spatial components of gene expression spanning embryonic development for all Caenorhabditis elegans genes and use it to determine the evolutionary ages of the germ layers. The gene expression program of the mesoderm is induced after those of the ectoderm and endoderm, thus making it the last germ layer both to evolve and to develop. Strikingly, the C. elegans endoderm and ectoderm expression programs do not co-induce; rather the endoderm activates earlier, and this is also observed in the expression of endoderm orthologues during the embryology of the frog Xenopus tropicalis, the sea anemone Nematostella vectensis and the sponge Amphimedon queenslandica. Querying the phylogenetic ages of specifically expressed genes reveals that the endoderm comprises older genes. Taken together, we propose that the endoderm program dates back to the origin of multicellularity, whereas the ectoderm originated as a secondary germ layer freed from ancestral feeding functions.
 
Overall design Two temporal assays of Caenorhabditis elegans embryonic development, starting at the zygote: (a) Embryos collected at fixed (~10 minute) time intervals. (b) Embryo segregates, up to five lines of blastomeres, isolated in reference to mitotic events. There were 184 samples in total, representing 100 distinct data points (50 in each assay).
 
Contributor(s) Hashimshony T, Feder MA, Levin M, Hall BK, Yanai I
Citation(s) 25487147
Submission date Sep 03, 2013
Last update date May 15, 2019
Contact name Itai Yanai
E-mail(s) yanai@technion.ac.il
Organization name Technion - Israel Institute of Technology
Department Biology
Lab Yanai
Street address Technion City
City Haifa
ZIP/Postal code 30200
Country Israel
 
Platforms (1)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
Samples (184)
GSM1221016 1_cell
GSM1221017 2_cell
GSM1221018 mpfc_010
Relations
BioProject PRJNA217930
SRA SRP029448

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50548_Blastomere_developmental_event_timecourse.tab.gz 2.3 Mb (ftp)(http) TAB
GSE50548_Full_experiment_expression.tab.gz 2.2 Mb (ftp)(http) TAB
GSE50548_Full_experiment_spikeins.tab.gz 13.9 Kb (ftp)(http) TAB
GSE50548_Whole_embryo_interval_timecourse.tab.gz 2.4 Mb (ftp)(http) TAB
GSE50548_c_elegans.WS230.annotations.gff3.gz 1.2 Mb (ftp)(http) GFF3
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Processed data are available on Series record
Raw data are available in SRA

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