Reprogramming of Human Fibroblasts into Hematopoietic Progenitors by Fusion With Human Fetal Liver CD34+ Cells (GenomeWideSNP_6)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Vladislav Sandler
PROVIDER: E-GEOD-23414 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2011-08-04 | E-GEOD-23416 | biostudies-arrayexpress
Project description:We present evidence for cytogenetic changes in two transformed ovarian surface epithelium cell lines, TOSE1 and TOSE4. hTERT-immortalised ovarian surface epithelial cell line spontaneously transformed as measured by growth in soft agar. These cells were grown on plastic, and genomic DNA was extracted and analyzed for cytogenetic changes. The genotyping Affymetrix SNP6.0 arrays were used to define copy number changes in the TOSE1 and TOSE4 cell lines.
2010-11-19 | E-GEOD-25492 | biostudies-arrayexpress
Project description:EZH2 is shown to be involved in regulation of DNA damage repair which may contribute to development of breast tumor initiating cells. To identify genomic aberrations regulated by EZH2 expression, we performed genome wide copy number variation analysis in breast tumor initiating cells expressing EZH2 compared to the vector control. This finding suggests EZH2 contributes to oncogenic amplification in breast tumor initiating cells. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from primary breast tumor initiating cells infected with EZH2 or Vector control constructs Copy number variation analysis of Affymetrix SNP 6.0 arrays was performed and compared between EZH2 and Vector control infected groups
2010-09-17 | E-GEOD-24144 | biostudies-arrayexpress
Project description:This data was used to identify regions of the genome that have undergone positive selection in a high-altitude Tibetan population. Affymetrix SNP arrays were used to genotype DNA extracted from blood samples. This data was used to perform genome-wide scans of positive selection in a native high-altitude Tibetan population.
2010-07-22 | E-GEOD-21661 | biostudies-arrayexpress
Project description:Finding gene associations in rare diseases is frequently hampered by the reduced numbers of patients accessible. Conventional gene-based association tests rely on the availability of large cohorts, which constitutes a serious limitation for its application in this scenario. To overcome this problem we have used here a combined strategy in which a functional association study (pathway-based analysis) has been conducted to prioritize candidate genes in a Spanish cohort of 53 trios of short-segment Hirschsprung's disease that have been further validated in a larger population of 146 trios. The study revealed a strong association of 10 gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other HSCR-related processes to the disease. A total of 10 new loci among the preselected candidates were found to be significantly associated to HSCR. This approach, based on the study of functionally-related gene sets, requires of lower sample sizes and opens new opportunities for the study of rare diseases. DNA derived from peripheral blood was hybridized to Affymetrix GeneChip® 500K mapping arrays. In total, 53 trios were analyzed consisting of affected child and their unaffected parents.
2012-03-18 | E-GEOD-33732 | biostudies-arrayexpress
Project description:Dnmt2 genes are highly conserved tRNA methyltransferases with biological roles in cellular stress responses. The absence of obvious mutant phenotypes under laboratory conditions suggested a function for Dnmt2 under non-physiological conditions. Indeed, Dnmt2 has recently been implicated in various aspects of the cellular stress response and the tRNA methyltransferase activity of Dnmt2 has been shown to interfere with stress-induced fragmentation of various tRNAs. We used adult animals and small RNA sequencing during a heat stress experiment to determine the tRNA fragment abundance and identities in wild-type and Dnmt2 mutant somatic tissues. Dnmt2 mutants produced tRNA fragments with different identities when compared to wild-type controls, indicating the accumulation of non-physiological tRNA-derived molecules in tissues without Dnmt2. 6 samples examined: heterozygous and Dnmt2 mutant under control, heat shock and recovery conditions
2012-11-12 | E-GEOD-35981 | biostudies-arrayexpress
Project description:In addition to KIT and PDGFRA mutations, sequential accumulation of other genetic events is involved in the development and progression of gastrointestinal stromal tumors (GISTs). Until recently, the significance of these other alterations has not been thoroughly investigated. The combination of gene expression profiling and high-resolution genomic copy number analysis offers a detailed molecular portrait of GISTs, providing an essential comprehensive knowledge necessary to guide the discovery of novel target genes involved in tumor development and progression. Fresh tissue specimens from 25 patients with GIST were collected and high-resolution genomic copy number analyses were performed using Affymetrix SNP array 6.0. GIST tumor samples from mutated (KIT or PDGFRA) or Wild Type patients were labeled for hybridization on Affymetrix microarrays. Copy number analysis of Affymetrix SNP6.0 arrays was performed for 25 GIST samples, then compared to gene expression data.
2010-08-27 | E-GEOD-20709 | biostudies-arrayexpress
Project description:Chordomas are rare, low to intermediate grade malignant bone tumors of the axial skeleton, believed to originate from the notochord. Treatment options are limited and mainly restricted to surgical excision, as chordomas have been proven to be largely resistant to conventional ionizing radiation and chemotherapy. Therefore a new cell line was established. The cell line has been characterized by immunohistochemistry,western blot and karyotyping using cobra fish technology. Copy number variations (CNV) and loss-of heterozygosity (LOH) from fibroblasts, tumor tissue, low and high cell line passage was evaluted by using Affymetrix 6.0SNP Arrays. DNA isolated from the patients MNCs was used as control. The cell line MUG-Chor1 is highly similar to genetic profiles of chordomas and provides therefore a powerful tool for further investigations. Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.
2012-07-11 | E-GEOD-25720 | biostudies-arrayexpress
Project description:Background: Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries. Methods: Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays and Illumina mRNA expression arrays as well as Illumina sequencing of the coding regions of 384 genes belonging to various pathways known to be altered in other cancers. Results: Genetic alterations were observed in the WNT, Hedgehog, cell cycle, DNA damage and epithelial-to-mesenchymal-transition pathways. Conclusions: The data suggests targeted therapies approved or in clinical development for gastric carcinoma would be of benefit to ~22% of the patients studied. In addition, the novel mutations detected here, are likely to influence clinical response and suggest new targets for drug discovery. DNA and RNA samples were obtained from hospitals in Russia and Vietnam according to IRB approved Protocols and with IRB approved consent forms from which informed consents were given for molecular and genetic analysis. The medical centres themselves also have internal ethical committees with reviewed the protocol and ICFs. The samples were sourced through Tissue Solutions Ltd (http://www.tissue-solutions.com/). Genotypes and copy number profiles were generated for each samples using 1 ug of DNA run on Affymetrix SNP V6 arrays using Affymetrix protocols.
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