Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene Expression Atlas for Human Embryogenesis

ABSTRACT: Gene expression profiling has provided critical insights into the molecular pathways underlying development of model organisms, however little information is available on regulated gene expression during human embryogenesis. We have now filled this important gap of knowledge by performing genome-wide microarray analysis of the Homo sapiens gene expression during the 4-9th week, a period when most organs develop. We analyzed individually 3 embryos for each of the 4th, 5th, 6th, 7th, 8th, and 9th week of human embryonic development by using the Affymetrix U133 plus 2.0 human GeneChip array.About half of all human genes are expressed and 18.6% of the expressed genes were significantly regulated during this important period. We further identified over 5000 regulated genes, most of which were previously not known to be associated with animal development. Our study also revealed that the genes involved here are distinct from those during early embryogenesis, which include three groups of maternal genes. Furthermore, we discovered that genes in a given developmental process are coordinately regulated. This led us to develop an easily searchable database of this entire collection of gene expression profiles, allowing for identification new genes important for a particular developmental process/pathway and deducing the potential function of a novel gene. The validity of the predictions from the database was demonstrated with two examples through spatiotemporal analyses of the two novel genes. Such a database should serve as a highly valuable resource for the molecular analysis of human development and pathogenesis. Human embryos were obtained from therapeutic termination of pregnancy induced by Mifepristone. Morphologically normal embryos were selected and staged according to the Carnegie classification and the Chinese embryonic developmental characteristics. Each whole embryo was micro-dissected from an intact trophoblast and stored directly in liquid nitrogen or homogenized using Trizol solution and then stored at -80oC. Total RNA was isolated from each whole embryo individually and each of the 3 RNA samples for each developmental time point was independently analyzed on a Human U133 plus 2.0 Genome Oligonucleotide Array.

ORGANISM(S): Homo sapiens

SUBMITTER: Wenxin Li

PROVIDER: E-GEOD-15744 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene expression atlas for human embryogenesis.

Yi Hong H Xue Lu L Guo Ming-Xiong MX Ma Jian J Zeng Yan Y Wang Wei W Cai Jin-Yang JY Hu Hai-Ming HM Shu Hong-Bing HB Shi Yun-Bo YB Li Wen-Xin WX

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 20100429 9

Human embryogenesis is believed to involve an integrated set of complex yet coordinated development of different organs and tissues mediated by the changes in the spatiotemporal expression of many genes. Here, we report a genome-wide expression analysis during wk 4-9 of human embryogenesis, a critical period when most organs develop. About half of all human genes are expressed, and 18.6% of the expressed genes were significantly regulated during this important period. We further identified >5000 ...[more]

PMID: 20430792

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Project description:The significant morphological differences observed during embryo development in angiosperms and gymnosperms are expected to be the result of a differential control of gene expression. We used a loblolly pine (Pinus taeda) cDNA microarray to analyze global transcriptional changes along zygotic embryogenesis in maritime pine (Pinus pinaster). A time-course analysis of the data obtained from the five embryo developmental groups used in this study led to the identification of 4,645 genes whose expression varied along P. pinaster embryogenesis. These transcripts were clustered into six distinct expression profiles. The grouping of these profiles in early, mid-embryogenesis and embryo maturation, according to the developmental period where most of the sequences were up-regulated, evidenced that characteristic transcriptional changes are associated to each developmental period. The application of a cut-off value of 1.95-fold change led to the identification of 1,838 differentially expressed transcripts that were categorized by biological process. Metabolism, interaction with the environment, oxidation-reduction and transport were some of the most represented categories. During early embryogenesis genes putatively involved in phytohormone-mediated signaling were identified, whereas in middle stages the overrepresented genes could be associated with cotyledon formation and induction of somatic embryogenesis. Genes associated with the synthesis of storage products were up-regulated in the latest stages of pine embryo development. It was also during this developmental period that the largest number of sequences putatively encoding transcription factors was identified. Pine immature zygotic embryos were pooled into five different developmental groups according to the collection date (Day0; Day5; Day11; Day15 and Day25). A common reference design was used. Total RNA was extracted from each sample. Three extractions were prepared per sample (biological replicates). A defined ammount from each RNA sample was pooled to use as reference. Messenger RNA was amplified for both test samples and reference. These were hybridized together in two separate experiments (technical replicates). In total, 30 slides were analyzed.

Dataset Information

Gene Expression Atlas for Human Embryogenesis

Publications

Gene expression atlas for human embryogenesis.

Similar Datasets

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