Transcription profiling of mouse developing placenta
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Kirstin Knox
PROVIDER: E-GEOD-11224 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Genomic evolution of the placenta using co-option and duplication and divergence.
Knox Kirstin K Baker Julie C JC
Genome research 20080313 5
The invention of the placenta facilitated the evolution of mammals. How the placenta evolved from the simple structure observed in birds and reptiles into the complex organ that sustains human life is one of the great mysteries of evolution. By using a timecourse microarray analysis including the entire lifetime of the placenta, we uncover molecular and genomic changes that underlie placentation and find that two distinct evolutionary mechanisms were utilized during placental evolution in mice a ...[more]
Similar Datasets
Project description:We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0). At each stage, the fetal placenta and maternal decidual tissues were dissected and profiled separately Experiment Overall Design: Mouse placentas were obtained from timed pregnant female mice at each timepoint, and fetal tissues were used to confirm embryo staging. Fetal placenta and maternal decidual tissues were dissected and pooled separately for each litter prior to RNA extraction and hybridization on Affymetrix microarrays.
2008-06-11 | E-GEOD-11220 | biostudies-arrayexpress
Project description:We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0). For these samples, at each stage the fetal placenta and maternal decidual tissues were dissected and profiled separately (See series 1). For this experiment (Series 2), placental and decidual timecourse samples were normalized and modeled with two undissected (including placental and decidual tissue) e17 placentas to allow for scaling of values for comparison to the undissected placenta samples used in the publicly available mouse GeneAtlas dataset Experiment Overall Design: Mouse placentas were obtained from timed pregnant female mice at each timepoint, and fetal tissues were used to confirm embryo staging. For all dissected samples, fetal placenta and maternal decidual tissues were dissected and pooled separately for each litter prior to RNA extraction and hybridization on Affymetrix microarrays.
2008-06-11 | E-GEOD-11222 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes between placentas from pregnancies with PE and placentas from normal pregnancies to search for the candiadate genes for further DNA methylation analysis The differentially expressed genes LEP and SH3PXD2A were further analyzed by DNA methylation. 5 placentas from pregnancies with PE and 7 from normal subjects were included in the gene expression microarray analysis.
2013-02-01 | E-GEOD-43942 | biostudies-arrayexpress
Project description:At an incidence of approximately 1/1000 births, neural tube defects (NTDs) comprise one of the most common and devastating congenital disorders. In an attempt to enhance and expand our understanding of neural tube closure, we undertook a high-throughput gene expression analysis of the neural tube as it was forming in the mouse embryo. Open and closed sections of the developing neural tube were micro-dissected from mouse embryos, and hybridized to Affymetrix mouse expression arrays. Clustering of genes differentially regulated in open and closed sections of the developing neural tube highlighted molecular processes previously recognized to be involved in neural tube closure and neurogenesis. Analysis of the genes in these categories identified potential candidates underlying neural tube closure. In addition, we identified approximately 25 novel genes, of unknown function, that were significantly up-regulated in the closed neural tube. Based on their expression patterns in the developing neural tube, five novel genes are proposed as interesting candidates for involvement in neurogenesis. The high-throughput expression analysis of the neural tube as it forms allows for better characterization of pathways involved in neural tube closure and neurogenesis, and hopefully will strengthen the foundation for further research along the pathways dictating neural tube development. Embryos were dissected at days E8.5 and E9.5, and the neuroepithelium/ neural tube were mechanically detached from underlying tissues, and then separated into two regions: 1) M-bM-^@M-^\open neuroepitheliumM-bM-^@M-^]: neuroepithelial tissue caudal to the open/closed junction, and 2) M-bM-^@M-^\closed neural tubeM-bM-^@M-^], extending from a somiteM-bM-^@M-^Ys breadth rostral to the open/closed junction, up to the level of the fifth- or sixth-to-last somite. Samples consisted of biological triplicates of RNA extract from the above tissues (pooled by litter, and representing a total of 111 embryos): E8.5 open neuroepithelium, E8.5 closed neural tube, E9.5 open neuroepithelium, and E9.5 closed neural tube. Thus, a total of 12 samples (representing 111 embryos) were hybridized to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix Inc., Santa Clara, CA, USA). One of the samples (06, closed E8.5) deviated significantly from the others in quality assessment and was therefore removed from subsequent analysis and not submitted to GEO.
2014-01-01 | E-GEOD-39442 | biostudies-arrayexpress
Project description:Background: Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes. Here we use a population genetics framework and next generation sequencing to evaluate how gene expression variation is apportioned among four human groups in a natural biological tissue, the placenta. Results: We estimate that on average, 33.2%, 58.9% and 7.8% of the placental transcriptome is explained by variation within individuals, among individuals and among human groups, respectively. Additionally, when technical and biological traits are included in models of gene expression they account for roughly 2% of total gene expression variation. Notably, the variation that is significantly different among groups is enriched in biological pathways associated with immune response, cell signaling and metabolism. Many biological traits demonstrated correlated changes in expression in numerous pathways of potential interest to clinicians and evolutionary biologists. Finally, we estimate that the majority of the human placental transcriptome (65% of expressed genes) exhibits expression profiles consistent with neutrality; the remainder are consistent with stabilizing selection (26%), directional selection (4.9%), or diversifying selection (4.8%). Conclusion: We apportion placental gene expression variation into individual, population and biological trait factors and identify how each influence the transcriptome. Additionally, we advance methods to associate expression profiles with different forms of selection. Placental mRNA was sequenced on an Illumina GAIIx. Samples were derived from 4 human groups, 10 individuals per group, 2 samples per individual
2015-03-07 | E-GEOD-66622 | biostudies-arrayexpress
Project description:In this study, we expand on this major advancement in O-GlcNAc enrichment protocols by adapting this approach to human-banked samples, which often presents their significant challenges. Indeed, patient samples are often banked without proper washing, thus contaminating cells with abundant O-glycosylated blood protein. These glycoproteins, such as human serum albumin, antibodies, and hemoglobin, pollute MS acquisition, masking the less abundant intracellular proteins and, even more, their O-GlcNAcylated forms. Thus, using freshly banked placentas, we present an adapted method to prepare human placental samples with naturally high blood content (13). We then enriched for O-GlcNAcylated protein using the PTMscan antibodies previously mentioned (12). However, our adapted protocol yielded over 60% of HexNAc peptide on total peptides. Per sample, we obtained up to 2,600 HexNAc-containing PSMs, 1,090 unique HexNAc peptides, and more than 1,000 unique HexNAc proteins using 45mg of starting placenta. Furthermore, we present a bioinformatic workflow to sort these HexNAc PSMs and extract the most confident O-GlcNAcylated proteins and sites. Thus, we confidentially identified 641 O-GlcNAcylated proteins, including up to 146 new proteins and 730 new sites within the 2 placental samples analyzed. Furthermore, we enriched for over 50 placenta-enriched O-GlcNAcylated proteins, such as RPA4, representing a new biomarker of the placental O-GlcNAcylation.
2024-02-14 | PXD047766 | Pride
Project description:STOX1B, the short protein-coding isoform of STOX1 (227 amino acids), has been shown to present opposite effects than the one of STOX1B in trophoblast cell models. Here, we investigate the overexpression of STOX1B in vivo in the mouse placenta. The changes accompany maternal effects on blood pressure and proteinuria reminiscent of preeclampsia, and effects of Intra Uterine Growth Restriction upon the foetuses.
2024-10-31 | E-MTAB-14457 | biostudies-arrayexpress
Project description:STOX1A overexpression in mice placenta triggers a preeclamptic phenotype in the mothers, with hypertension, proteinuria and kidney alterations (Doridot et al, Hypertension, 2013), this being connected with NO depletion and increase of nutrosative stress (Doridot et al, Antiox Redox Signal, 2014). Tetrahydrobiopterin (BH4) is a cofactor essential for NO production. We treated preeclamptic mice with this drug, and analyzed placental gene expression in four groups (Control mice, Control mice with BH4, Preeclamptic mice and preeclamptic mice with BH4).
2021-05-01 | E-MTAB-9314 | biostudies-arrayexpress
Project description:An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human placenta and mouse placenta show structural similarities but there has been no systematic attempt to assess their molecular similarities or differences. We built a comprehensive database of protein and microarray data for the highly vascular exchange region micro-dissected from the human and mouse placenta near-term. Abnormalities in this region are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ~5% of all pregnancies. To compare the gene expression patterns in the vascular exchange regions of the human (villus tree) and mouse (labyrinth) placenta. Experiment Overall Design: Mouse labyrinth tissue was micro-dissected form naturally mated crosses of C57Bl/6J mice. Placentas were individually dissected on embryonic day 17.5. From each litter ¼ of the tissue were set aside for RNA extraction and microarray analysis and ¾ for cellular fractionation and proteomic analysis, as recently described (Kislinger et al., 2006). Human villous trees were dissected from term normal placenta delivered by cesarean section from a term pregnancy (~ 38 weeks). Tissue was divided for organellar fractionation and RNA extraction.
2009-06-22 | E-GEOD-13155 | biostudies-arrayexpress
Project description:Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, the transcriptional landscape of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide expression profile of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, prioritized stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling the bioinformatics of the congenital heart disease interactome, we deconstructed disease-centric regulatory networks encoded within this cardiogenic atlas to reveal stage-specific developmental disturbances clustered on epithelial-to-mesenchymal transition (EMT), BMP regulation, NF-AT signaling, TGFb-dependent induction, and Notch signaling. Therefore, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. To interrogate the temporal and spatial expression profiles across the entire genome during mammalian heart development, we designed a time-course microarray experiment using the mouse model at defined stages of cardiogenesis, starting with embryonic stem cells (ESC, R1 stem cell line), early embryonic developmental stages: E7.5 whole embryos, E8.5 heart tubes, left and right ventricle tissues at E9.5, E12.5, E14.5, E18.5 to 3 days after birth (D3) and adult heart (Figure 1A). At each time point, microarray experiments were performed on triplicate biological samples. Starting at E9.5, tissue samples from left ventricles (LV) and right ventricles (RV) were microdissected for RNA purification and microarray analysis to determine spatially differential gene expression between LV and RV during heart development.
2014-05-19 | E-GEOD-51483 | biostudies-arrayexpress