Gene expression comparison between fibroblasts samples of control and SPOAN affected patients
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE67527 | GEO | 2015/04/03
SECONDARY ACCESSION(S): PRJNA280161
REPOSITORIES: GEO
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Project description:Objective: Analyze expression patterns of genes located at linkage region of SPOAN syndrome (11q12-13), in order to identify genes differentially expressed in samples of SPOAN individuals compared to healthy controls. Fibroblast samples of 8 samples where analyzed: 4 SPOAN affected patients and 4 healthy controls. There are no replicates and there are not affected and control from the same patient.
2015-04-03 | E-GEOD-67527 | biostudies-arrayexpress
Project description:Genome-wide association study (GWAS) was performed in 120 patient-parents trio samples from Japanese schizophrenia pedigrees ABSTRACT: Schizophrenia is a devastating neuropsychiatric disorder with genetically complex traits. Genetic variants should explain a considerable portion of the risk for schizophrenia, and genome-wide association study (GWAS) is a potentially powerful tool for identifying the risk variants that underlie the disease. Here, we report the results of a three-stage analysis of three independent cohorts consisting of a total of 2,535 samples from Japanese and Chinese populations for searching schizophrenia susceptibility genes using a GWAS approach. Firstly, we examined 115,770 single nucleotide polymorphisms (SNPs) in 120 patient-parents trio samples from Japanese schizophrenia pedigrees. In stage II, we evaluated 1,632 SNPs (1,159 SNPs of p < 0.01 and 473 SNPs of p < 0.05 that located in previously reported linkage regions). The second sample consisted of 1,012 case-control samples of Japanese origin. The most significant p value was obtained for the SNP in the ELAVL2 [(embryonic lethal, abnormal vision, Drosophila)-like 2] gene located on 9p21.3 (p = 0.00087). In stage III, we scrutinized the ELAVL2 gene by genotyping gene-centric tagSNPs in the third sample set of 293 family samples (1,163 individuals) of Chinese descent and the SNP in the gene showed a nominal association with schizophrenia in Chinese population (p = 0.026). The current data in Asian population would be helpful for deciphering ethnic diversity of schizophrenia etiology. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples. SUPPLEMENTARY FILES: CEL files were processed by manufacture's protocol. Genotype data were analyzed with the GeneSpring GT (Varia) 2.0 software package developed by Agilent Technologies (Santa Clara, CA). Matrix tables for the Genetic programs were produced (Linkage format: http://bioinformatics.med.utah.edu/~alun/software/docs/linkage.html) File 1: Matrix file_SNP_Map.txt File 2: Matrix file_Family_Information.txt File 3: Matrix file_Pedigree_Format.txt (Genotyping data of Linkage format) Transmission disequilibrium test was performed using the R program (http://www.r-project.org). File 4: Matrix file_results.txt
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2010-02-24 | GSE7214 | GEO
Project description:BACKGROUND:Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points. METHODS:Fibroblasts from skin biopsies of 15 cell donors were exposed to a high (2Gy) and a low (0.05Gy) dose of X-rays. RNA was extracted and sequenced 2?h and 4?h after exposure. Differentially expressed genes with an adjusted p-value <?0.05 were flagged and used for pathway analyses including prediction of upstream and downstream effects. Principal component analyses were used to examine the effect of two different sequencing runs on quality metrics and variation in expression and alignment and for explorative analysis of the radiation dose and time point of analysis. RESULTS:More genes were differentially expressed 4?h after exposure to low and high doses of radiation than after 2?h. In experiments with high dose irradiation and RNA sequencing after 4?h, inactivation of the FAT10 cancer signaling pathway and activation of gluconeogenesis I, glycolysis I, and prostanoid biosynthesis was observed taking p-value (<?0.05) and (in) activating z-score (?2.00 or???-?2.00) into account. Two hours after high dose irradiation, inactivation of small cell lung cancer signaling was observed. For low dose irradiation experiments, we did not detect any significant (p?<?0.05 and z-score???2.00 or???-?2.00) activated or inactivated pathways for both time points. CONCLUSIONS:Compared to 2?h after irradiation, a higher number of differentially expressed genes were found 4?h after exposure to low and high dose ionizing radiation. Differences in gene expression were related to signal transduction pathways of the DNA damage response after 2?h and to metabolic pathways, that might implicate cellular senescence, after 4?h. The time point 4?h will be used to conduct further irradiation experiments in a larger sample.
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2010-03-09 | E-GEOD-7214 | biostudies-arrayexpress
Project description:Mycetoma is a lifelong granulomatous disease of subcutaneous tissues and bones. Histopathology is a substantiated indicative method based on the assumption of a definitive diagnosis of mycetoma. It requires efficient processing of tissues including bone decalcification. The decalcification process must ensure complete removal of calcium and also a proper preservation of tissue and microorganisms' staining ability. Objectives. To compare the conventional method used in decalcification with the microwave method using different decalcification solutions. Different characteristics were tested, including the speed of decalcification and morphological and fungal preservation in bone tissue affected with mycetoma. Materials and Methods. Three decalcification solutions were employed to remove calcium from 50 bone tissue samples affected with mycetoma, including 10% neutral buffered EDTA (pH 7.4), 5% nitric acid, and 5% hydrochloric acid. Conventional and microwave methods were used. Haematoxylin-eosin (HE) stain, Gridley's stain, and Grocott hexamine-silver stain were employed to evaluate the bone and fungi morphologies. Results. The decalcification time of the conventional method compared with the microwave method with 10% EDTA (pH 7.4) took 120 hours and 29 hours, while 5% hydrochloric acid and 5% nitric acid took 8 hours and 3 hours, separately. Also, 10% EDTA is the best decalcifying agent for HE staining and fungal stains. 5% hydrochloric acid and 5% nitric acid can be used for fungal staining. Conclusion. The current study investigated the effects of different decalcifying agents as well as two decalcification procedures on the preservation of the bone structure and fungal staining, which will help to develop suitable protocols for the analyses of the bone tissue affected with mycetoma infection.
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