Protoarray based identificatoin of dysregulated proteins in metastatic osteosarcoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE78192 | GEO | 2016/02/24
SECONDARY ACCESSION(S): PRJNA312894
REPOSITORIES: GEO
Similar Datasets
Project description:Glaucoma is the leading cause of irreversible blindness worldwide. An early diagnosis of the disease is crucial for treatment success. Mechanisms behind glaucoma pathogenesis are not completely understood, but disease related alterations in the serological autoantibody profile indicate an immunologic component. These changes in immunoreactivity may serve as potential biomarkers. Therefore, a serological proteome analysis (SERPA) approach was used to identify novel autoantibody biomarker candidates in primary open angle glaucoma. Autoantibodies in individual sera samples of glaucoma patients and control were analysed by serological proteome analysis (SERPA) using porcine trabecular meshwork (TM) tissue lysates as antigen source. Immunoblot spot intensities were computed by “Delta2D” (Decodon) and spots of interest were matched with preparative 2DE gels and identified by mass spectrometry to identify the potential autoantigens.
2019-02-21 | PXD011752 | Pride
Project description:Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design
2006-01-05 | GSE3973 | GEO
Project description:Mass spectrometry analysis of immunoreactive protein spots revealed that seveal prostate cancer patient sera had autoantibodies to a number of proteins associated with both the glycolysis and plasminogen pathways.
2017-01-06 | PXD003968 | Pride
Project description:Signal intensities of BC-GP array for 105 speimens The Verigene Gram-Positive Blood Culture (BC-GP) nucleic acid assay is an automated microarray-based test, which can detect 12 Gram-positive bacterial genes and 3 resistance determinants using blood culture broths. We investigated signal intensities of microarray spots, and reclassified undetermined results where the automated system failed and various errors were called in blood culture specimens and spiked samples.
2014-05-30 | GSE57245 | GEO
Project description:Osteosarcoma (OS) is the most common primary bone tumour in children and young adults, and the second highest cause of cancer-related death in this age group. In spite of aggressive chemotherapy, disease-free survival has not improved significantly in the past 20 years, and 50% of patients subsequently develop fatal pulmonary metastasis. We have performed gene expression profiling of primary osteosarcoma biopsies (i) to identify prognostic markers, and (ii) to identify novel therapeutic targets. Keywords: Comaprison between disease status (metastatic vs non-metastatic) and normal
2010-08-30 | GSE9508 | GEO
Project description:Osteosarcoma (OS) is the most common primary bone tumour in children and young adults, and the second highest cause of cancer-related death in this age group. In spite of aggressive chemotherapy, disease-free survival has not improved significantly in the past 20 years, and 50% of patients subsequently develop fatal pulmonary metastasis. We have performed gene expression profiling of primary osteosarcoma biopsies (i) to identify prognostic markers, and (ii) to identify novel therapeutic targets. Keywords: Comaprison between disease status (metastatic vs non-metastatic) and normal Two-colour experiment. 7 samples for non-metastatic patients, 6 of which are analyzed in duplicate (dye-swaps); 11 samples for metastatic patients, 10 of which are analyzed in duplicate (dye-swaps); 5 samples of non-malignant bone analyzed individualy, no dye-swaps (i.e. 5 biological replicates).
2010-08-30 | E-GEOD-9508 | biostudies-arrayexpress
Project description:Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching complementary sequence and other spots with one or two mismatches: in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays. Keywords: experiment to assess technical aspects of hybridization in microarrays
2009-03-01 | GSE14547 | GEO
Project description:Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye.
2005-11-01 | E-SMDB-2652 | biostudies-arrayexpress
Project description:This study was conducted to identify dysregulated genes associated with acquired resistance to chemotherapy. Endoscopic biopsy samples were collected from CF-treated metastatic gastric cancer patients prior to therapy and following the development of resistance to therapy.
2011-06-01 | E-GEOD-14209 | biostudies-arrayexpress
Project description:A total of 10 male Fischer 344 rats, 5 weeks old, were purchased from Charles River Japan, Incorporated, Atsugi, Kanagawa, Japan. Rats were divided into 2 groups each consisting of 5 animals housed in a plastic cage with white flake bedding in an air-conditioned room. Rats were used for the experimentation after a 1-week acclimation on a basal diet (CRF-1, Oriental Yeast Corporation, Itabashi, Tokyo, Japan) and allowed free access to food and tap water throughout the acclimation and experimental periods. Body weight, food consumption, and water intake were monitored weekly. The CDAA diet was obtained from Dyets, Bethlehem, PA. After acclimation, group 1 rats were administered the basal diet, while group 2 rats were placed on the CDAA diet for 70 weeks and then sacrificed. The livers were taken and macroscopically examined. Portions of group 1 livers, as well as the macroscopic tumors and their surrounding, non-cancerous tissues of group 2 livers were fixed in 10% neutrally-buffered-formalin for 24 hours, embedded in paraffin, processed for the routine hematoxylin-and-eosin staining procedure, and histologically examined. Remaining portions of these 3 types of liver tissues were immediately frozen in liquid nitrogen and stored at -80C. Group 1 liver tissues, group 2 liver tissues from non-cancerous areas, and group 2 liver tissues from tumors (after histologically diagnosed as HCCs; see the results section) were used as normal liver samples, surrounding non-cancerous liver samples, and HCC samples, hereafter referred to as CON, NC, and CA, respectively. The microarray and RT-PCR experiments and the subsequent data analysis were performed using 5 CON samples from individual group 1 rats and 5 matched pairs of NC and CA samples from individual group 2 animals. RNA Isolation and Probe Labeling. Total RNA from liver tissues was isolated using RNeasy Midi kits (QIAGEN, Hilden, Germany). The integrity of the RNA was checked by electrophoresis on 1% agarose-formaldehyde gels. Five micrograms of total RNA from individual samples were labeled with Cy3 (Amersham Biosciences, Uppsara, Sweden) using BD Atlas Powerscript Fluorescent Labeling kits (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer’s protocols. Hybridization, Scanning, and Quantification. Cy3-labeled probes were hybridized to Atlas Rat 3.8 I microarrays (BD Biosciences Clontech) containing 3757 genes for 16 hours at 50C. After hybridization, microarrays were washed, dried, and scanned using a GMS 418 confocal laser scanner (Genetic MicroSystems, Woburn, MA). Fluorescence intensities of the Cy3 channels were quantified using ImaGene 4.0 software (BioDiscovery, El Segundo, CA). Data analysis was performed using the GeneSpring software, version 5.1 (Silicon Genetics, Redwood City, CA), including appropriate statistics. Dividing by the median calculated from all of the signal intensities for the Cy3 in a given sample normalized the fluorescence signal for each gene. The VALUEs for each gene was then calculated by dividing the normalized signal by the median of each gene to offset differences in expression levels between genes. Keywords: parallel sample
2005-02-01 | GSE1946 | GEO