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E-GEOD-18887 - Transcriptome Profiling of Human Embryos during Early Organogenesis

Released on 18 March 2010, last updated on 2 May 2014
Homo sapiens
Samples (18)
Array (1)
Protocols (6)
We here report transcriptome profiling of human embryos at six successive developmental stages (i.e., Carnegie Stages 9 to 14), representing the first comprehensive gene expression database of early human organogenesis. Through a series of data mining and comparisons with the transcriptome during mouse embryogenesis and the disparate genomic data in human embryonic stem cells, we revealed that development potential during early human organogenesis is orchestrated by two dominant categories of genes. Specifically, most gradually induced genes are largely differentiation related whereas those gradually repressed are involved in both stemness- and differentiation-relevant aspects of the developmental potential. Further through integrative mining we uncovered a molecular network that well characterizes stemness- and differentiation-relevant aspects of developmental potentials during early human organogenesis. Analysis of published data showed that the network could serve to evaluate various differentiation models. Our results make a significant step towards understanding of human embryogenesis at a molecular level and suggest that developmental potentials are under control of shared regulatory events. With the consent of subjects and of the Ethical Review Board of the Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine,we collected human post-implantation embryos at six successive time periods: Carnegie Stages 9 to 14 (E20 to E32), covering the first third of organogenesis. Using the Affymetrix HG-U133A Genechip microarrays, three replicates were independently profiled for each stage to minimize the influence of the embryo-to-embryo variation. Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization. The resultant expression data were imported into Extraction of Differential Gene Expression (EDGE) software for the detection of probesets exhibiting the consistent changes within the triplicates and differential expression (denoted as hORG expression matrix). The hORG expression matrix was subjected to Linear Models for Microarray Data (LIMMA) bioconductor library for identification of stage-transitive transcriptome changes, and self-organizing map combined with singular value decomposition (SOM-SVD) as well as SOM-based two-phase gene clustering for the topology-preserving extraction of temporal expression patterns. Hypergeometric distribution-based enrichment analyses were performed to explore the underlying biological relevance of gene groups of interest using diverse external annotated databases. The Cytoscape plug-in jActiveModules was modified to identify expression-active connected subnetworks in the compiled human interaction/association network.
Experiment type
transcription profiling by array 
Hai Fang <>, Chunliang Li, Gang Jin, Ji Zhang, Kankan Wang, Shijun Fu, Ying Jin, Ying Yang, Zhuqing Yang
Investigation descriptionE-GEOD-18887.idf.txt
Sample and data relationshipE-GEOD-18887.sdrf.txt
Raw data (1)
Processed data (1)
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-18887.eSet.r