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.
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
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.
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
Project description:Tetra-acetylated Histone H4 ChIP-chip performed on GM06990 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
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
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.
Project description:This SuperSeries is composed of the following subset Series: GSE29517: ChIP-chip from Drosophila egg chambers using ORC2 antibody GSE29518: ChIP-chip from dissected Drosophila egg chambers using antibody recognizing RNAPII GSE29520: ChIP-chip from Drosophila egg chambers using antibody recognizing tetra-acetylated histone H4 GSE29526: Expression profile of 16C ovarian follicle cells Refer to individual Series