Project description:The genome of 14 vulvar SCC was analyzed by aCGH and microarray to identify common imbalances present in the tumors as well as which genes were deregulated. Overall there was a good concordance between the imbalances scored by aCGH and the level of gene expression found by microarray, i.e., the genes located in gained regions were overexpressed while those located in lost regions were found down-regulated. The whole-gene expression profile of 14 SCC of the vulva was compared to 5 normal vulvar samples to identify genes that were deregulated in the tumors genome. Vulvar hyperplasia 03-48 not further analyzed and not included in the normalized data but included in the non-normalized data
Project description:The whole-gene expression profile of 24 endometrial stroma sarcol was used to identify genes that were deregulated in the tumors genome. The analysis was performed comparing the high-grade to the low-grade tumors.
Project description:The imbalances scored by arrayCGH mapped to different chromosomes with losses being more common than gains. Frequent losses of large chromosomal segments were scored from 3p and 8p whereas same-sized gains were frequent from 3q and 8q. This is the first study of vulvar tumors using arrayCGH, and some frequent imbalances could be defined precisely. 14 patients we analyzed without replicates against a commercial common reference.
Project description:Transcriptome analysis in HEK293T transfected with plasmid carrying different isoforms of BPIFB4 gene. This gene was previously associated with exceptional longevity in a GWAS study performed on three different populations. Results indicate an up-regulation of stress response genes and proteostasis genes in HEK293T transfected with plasmid carrying the longevity-associated variant (LAV) of BPIFB4. Total RNA obtained from HEK293T over-expressing wild-type or mutated form of BPIFB4.
Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome. aCGH control vs. patient, total of 7 patients Lowest normalized log2 ratio = patient 1: -1.99; patient 2: -1.87; patient 3: -2.16; patient 4: -2.11; patient 5: -1.974802452; patient 6: -2.23; patient 7: -1.36.
Project description:Osteosarcoma (OS) is the primary bone tumor in children and young adults. Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from human cases of OS to identify a profile of differentially expressed miRNAs. Comprehensive miRNA expression profiling was completed using the Exiqon miRNome platform (human panels I+II, V3) on 20 disease samples (10 localized, 10 metastatic) and 15 healthy controls.
Project description:Osteosarcoma (OS) is the primary bone tumor in children and young adults. Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from a genetically engineered mouse model of OS to identify a profile of four plasma miRNAs. Plasma from mice with OS were profiled for miRNAs and compared with the profile of plasma from disease-free mice
Project description:10 biopsies from one patient undergoing a auxiliary liver and combined kidney transplantation, where one liver lobe is replaced by an auxiliary liver lobe. Thereafter the kidney is transplanted. Keywords: Time course study 10 samples, no replicates.
Project description:Through ChIP-Seq analysis with the Illumina Whole Genome Analyzer, we identify binding sites for P300 (EP300) and CBP (CREBBP) in Human glioblastoma T98G cells that were cell cycle synchronized before and after stimulation. In our analysis, we focused on the identification of genes differentially bound by P300 and CBP. ChIP-seq with P300 and CBP antibodies over 2 timepoints