Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

In vivo rabbit preimplantation development

ABSTRACT: Evaluation of the transcriptomic profile of the rabbit embryo along the preimplantation period during in vivo development. Three embryonic stages were used: four cell embryos (H32 post-coïtum); morula (H58 pc) and blastocyst (H90 pc). Keywords: time course rabbit embryo 18 samples

ORGANISM(S): Oryctolagus cuniculus

SUBMITTER: Duranthon Veronique

PROVIDER: E-GEOD-12084 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Revealing the dynamics of gene expression during embryonic genome activation and first differentiation in the rabbit embryo with a dedicated array screening.

Léandri R D RD Archilla C C Bui L C LC Peynot N N Liu Z Z Cabau C C Chastellier A A Renard J P JP Duranthon V V

Physiological genomics 20081111 2

Early mammalian development is characterized by extensive changes in nuclear functions that result from epigenetic modifications of the newly formed embryonic genome. While the first embryonic cells are totipotent, this status spans only a few cell cycles. At the blastocyst stage, the embryo already contains differentiated trophectoderm cells and pluripotent inner cell mass cells. Concomitantly, the embryonic genome becomes progressively transcriptionally active. During this unique period of dev ...[more]

PMID: 19001509

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Project description:Data presented here show that gene expression in the mouse brain changes during systemic infection relative to a steady state (uninfected control) mouse during systemic Listeria monocytogenes infection. Microarray analysis of gene expression in the brain following i.v. inoculation of 1-2 LD 50 L. monocytogenes showed changes in brain transcriptional activity occurred prior to brain infection. Keywords: infectious diseases model, gene expression profiling for cell signaling/trafficking Mice were injected with 1-2 LD50 wild type L. monocytogenes or with sterile PBS (control) then seven animals from each group were harvested daily for 4 days. From each day, groups of five infected animals were selected for microarray analysis based upon similarities in CFU bacteria in the spleen (day 1), blood (day 2), and brain (days 3 and 4) and were randomly paired with brains harvested from control animals. RNA was extracted from the brain halves using the Atlasâ¢ Pure Total RNA Labeling System and hybridized to plastic slides with 32P-labeled probes using Atlasâ¢ Plastic Mouse 5K Microarray (Clontech, Mountain View, CA) according to the manufacturerâs directions. Hybridization to the arrays and phosphorimaging analysis were performed in the OUHSC microarray facility. Phosphorimaging analysis was performed using a Stormâ¢ optical scanner (Molecular Dynamics Inc., Sunnyvale, CA), and initial background corrections were performed using the Array Vision Software (Imaging Research Inc., St. Catharines, Ontario). Data analyses were performed using Genespring GX v. 7.3 (Agilent Technologies, Palo Alto, CA). Raw signal data were normalized to the median of the entire chip for each sample, and all samples were further normalized per gene to the medians of data from the uninfected samples. Data for each day were analyzed by Mann Whitney Wilcoxen nonparametric test with a p-value cutoff of 0.05. Lists of genes were generated to reflect 2, 3, or 5-fold upregulation and downregulation based on significance. Expression data were incorporated into Ingenuity software (Ingenuity Systems, Inc., Redwood City, CA) to enable further understanding of complex relationships as well as provide further information about key canonical pathways in which the genes of interest functions.

Project description:In addition to nourishing the embryo, extra-embryonic tissues (EETs) contribute to early embryonic patterning, primitive hematopoiesis, and fetal health. These tissues are of major importance for human medicine, as well as for efforts to improve livestock efficiency, but they remain incompletely understood. In bovines, EETs are accessible easily, in large amounts, and prior to implantation. We took advantage of this system to describe, in vitro and in vivo, the cell types present in bovine EETs at Day 18 of development. Specifically, we characterized the gene expression patterns and phenotypes of bovine extra-embryonic ectoderm (or trophoblast; bTC), endoderm (bXEC), and mesoderm (bXMC) cells in culture and compared them to their respective in vivo micro-dissected cells. After a week of culture, certain characteristics (e.g., gene expression) of the in vitro cells were altered with respect to the in vivo cells, but we were able to identify “cores” of cell-type-specific (and substrate-independent) genes that were shared between in vitro and in vivo samples. In addition, many cellular phenotypes were cell-type-specific with regard to extracellular adhesion. We evaluated the ability of individual bXMCs to migrate and spread on micro-patterns, and observed that they easily adapted to diverse environments, similar to in vivo EE mesoderm cells, which encounter different EE epithelia to form chorion, yolk sac, and allantois. With these tissue interactions, different functions arose that were detected in silico and corroborated in vivo at D21-D25. Moreover, analysis of bXMCs allowed us to identify the EE cell ring surrounding the embryonic disc (ED) at D14-15 as mesoderm cells, which had been hypothesized but not shown prior to this study. We envision these data will serve as a major resource for the future in the analysis of peri-implanting phenotypes in response to the maternal metabolism and contribute to subsequent studies of placental/fetal development in eutherians. Amplified material was indirectly labelled using "random" hexamers. One independent target was generated and hybridised onto one array. 1-3 measurements per cell type were generated.

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Dataset Information

In vivo rabbit preimplantation development

Publications

Revealing the dynamics of gene expression during embryonic genome activation and first differentiation in the rabbit embryo with a dedicated array screening.

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