Tetra-Amelia with lung aplasia phenotype
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ABSTRACT:
PROVIDER: PRJNA438127 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Clinical findings of this case has been reported previously by Sergio de Sousa (American Journal of Medical Genetics Part A 146A:2799–2803 (2008)). RSPO2 gene has been identified by our group (İstanbul, Turkey, 2014) as responsible gene for Tetra-Amelia with lung aplasia phenotype. To find causative pathogenic variations, sanger sequencing of fetal DNA was performed and did not reveal any variations. 300K SNP array was performed to analyse possible CNVs. A homozygous 154kb deletion on chr8 (deletion break points:108,809,266-108,963,256) covering intron 5 (partial), exon 6 and 3'UTR (partial) of RSPO2 gene was identified as the causative deletion.
2018-04-04 | GSE111781 | GEO
Project description:Chromatin immunoprecipitation of tetra-acetylated histone H4 followed by hybridization to genome-wide tiling microarrays demonstrated that tetra-acetylated H4 is enriched at the two chorion Drosophila amplicons in follicle cells (DAFC) as well as other non-amplified loci
2011-05-27 | GSE29520 | GEO
Project description:To more accurately model inhalation toxicity in vitro, we developed a tetra-culture system that combines lung alveolar epithelial cells, endothelial cells, macrophages, and mast cells in a three-dimensional orientation. We characterized the influence of the added complexity, using network perturbation analysis and gene expression data, to gain an insight into the steady-state profile of the assembled complete three-dimensional model using all four cell types and of simpler models of one, two, or three of the cell types. Gene expression data were analyzed using cause-and-effect biological network models, together with a quantitative network-scoring algorithm to determine the biological impact of co-culturing the various cell types. In the assembled tetra-culture, macrophages appeared to be the largest contributors to overall network perturbations, promoting high basal levels of oxidative stress and inflammation. This finding led to further optimization of the model using rested macrophages; the addition of rested macrophages decreased the basal inflammatory and cell stress status of the co-culture. Finally, we compared transcriptional profiles from publicly available datasets of conventional in vitro models representative of the airways and of healthy human lung tissues, to assess similarities between our model and other in vitro models and the human lung. On the transcriptional level, we found an increasing correlation between airway models and normal human lung tissue, particularly as cell types became more physiologically relevant and the complexity of the system increased. This indicates that the combination of multiple lung-relevant cell types in vitro does indeed increase similarity to the physiological counterpart.
2019-02-12 | E-MTAB-7072 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation of tetra-acetylated histone H4 followed by hybridization to genome-wide tiling microarrays demonstrated that tetra-acetylated H4 is enriched at the two chorion Drosophila amplicons in follicle cells (DAFC) as well as other non-amplified loci Comparison of tetra-acetylated H4 ChIP sample compared to input DNA for two different Drosophila strains
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Project description:The somatic microenvironment supports spermatogonial stem cell differentiation into sperm. Extracellular matrix (ECM) plays multiple roles in the stem cell niche, including self-renewal, proliferation, differentiation and survival of spermatogonial cells. The pathophysiology of male infertility might be representative of a progressive degenerative process of the testicular tissue, including ECM, rather than a defective genetic background, thus outlining the existence of chronic etiological agents/pathways. In this context, we sought to identify potential causative factors responsible for a number of modifications of the testicular somatic microenvironment associated with idiopathic germ cell aplasia in human beings. Proteomic analysis of the decellularized ECM was performed to study testis parenchyma from 10 idiopathic non-obstructive azoospermic (iNOA) men, dichotomized according to positive sperm retrieval versus germ cell aplasia. Germ cell aplasia was characterized by an increased nuclear distribution of the retinoic acid receptor in Sertoli cells which was associated with decreased expression of the ECM markers, Nidogen-2 and Heparan sulfate proteoglycan-2. Decreased levels of the interstitial matrisome associated Factor IX and its regulator VKORC1 were instead coupled with decreased signaling of vitamin K in Leydig cells. This study identified pathogenetic signature of the somatic testicular microenvironment and provide mechanistic insights into the molecular determinants of human idiopathic germ cell aplasia.
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Project description:Germ cell aplasia represents the most severe form of male infertility, and is associated with increased risk of early onset age-related chronic diseases and higher risk of death. Here we investigated the transcriptional landscape of 3880 somatic cells clustered in Sertoli, peritubular Myoid, Leydig, endothelial, stromal, T cells and macrophages from 3 human testis with idiopathic germ cell aplasia. Deregulated somatic pathways were associated with over-expression of paternally imprinted genes in immature Leydig cells, extracellular matrix composition and organization, hormonal milieu, chronic pro-inflammatory environments and early ageing, which were validated with an external cohort of 44 men with idiopathic germ cell aplasia compared to 102 age-matched fertile men. These 7 transcriptomic datasets unveil new insights into the germ cell aplasia, and prompts new thinking to better understand the pathogenesis of the idiopathic disease and the associated clinical manifestations of early ageing process.
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Project description:Tetra-acetylated Histone H4 ChIP-chip performed on HeLaS3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Acetylated Histone H4-binding regions. Use of this data requires permission from its producers. Keywords: ChIP-chip
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Project description:Gene expression profiling reveals a potential role of SQ, Tri-SQ, and Tetra-SQ in stimulating hair growth in dermal papilla cells. Squalene (SQ) was found to exhibit a strong antioxidant and anti-inflammatory activity; however, its biological effects is underestimated because of its insolubility. To overcome this problem, new amphiphilic SQ derivatives were synthesized and were used in this study to check their potential effect in vitro and in vivo on inducing hair growth while exhibiting an anti-aging property.
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