Juvenile Rheumatoid Arthritis Profiles In PBMC and SFMC
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE1402 | GEO | 2004/08/11
SECONDARY ACCESSION(S): PRJNA90185
REPOSITORIES: GEO
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Project description:Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA). 57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
2007-08-14 | E-GEOD-1402 | biostudies-arrayexpress
Project description:Analysis of gene expression in Ws-0 lec1 (LEAFY COTYLEDON1) mutant Arabidopsis thaliana. Developmental stages studied includes 24-Hr post-fertilization, globular stage, cotyledon stage, mature green stage, post-mature green stage, and seedlings. Microarray Methods: Total RNA was extracted using the Hot Borate Method [Stones et. al. PNAS vol 98 no 20: 11806-11811 (2001)]. Biotinylated cRNA were prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit (Farmingdale, NY). cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips. The scanned array images were analyzed using Affymetrix Microarray Suite 4.0 (MAS 4.0) with a global scaling intensity set at 500. Keywords: other
2005-01-01 | GSE1051 | GEO
Project description:Objective. Microarray analysis was used to determine whether children with recent onset polyarticular juvenile idiopathic arthritis (JIA) exhibit biologically or clinically informative gene expression signatures in peripheral blood mononuclear cells (PBMC). Methods. Peripheral blood samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents. RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips. Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization. Results. Initial analysis revealed 873 probe sets for genes that were differentially expressed between polyarticular JIA and controls. Hierarchical clustering of these probe sets distinguished three subgroups within polyarticular JIA. Prototypical subjects within each subgroup were identified and used to define subgroup-specific gene expression signatures. One of these signatures was associated with monocyte markers, another with transforming growth factor-beta-inducible genes, and a third with immediate-early genes. Correlation of these gene expression signatures with clinical and biological features of JIA subgroups suggests direct relevance to aspects of disease activity and supports the division of polyarticular JIA into distinct subsets. Conclusions. PBMC gene expression signatures in recent onset polyarticular JIA reflect discrete disease processes and offer a molecular classification of disease. Keywords: Patient vs. control, reassessment of phenotype PBMC samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents. RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips. Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization.
2009-06-30 | E-GEOD-13849 | biostudies-arrayexpress
Project description:Objective. Microarray analysis was used to determine whether children with recent onset polyarticular juvenile idiopathic arthritis (JIA) exhibit biologically or clinically informative gene expression signatures in peripheral blood mononuclear cells (PBMC). Methods. Peripheral blood samples were obtained from 59 healthy children and 61 children with polyarticular JIA prior to treatment with second-line medications, such as methotrexate or biological agents. RNA was purified from Ficoll-isolated mononuclear cells, fluorescently labeled and then hybridized to Affymetrix U133 Plus 2.0 GeneChips. Data were analyzed using ANOVA at a 5% false discovery rate threshold after Robust Multi-Array Average pre-processing and Distance Weighted Discrimination normalization. Results. Initial analysis revealed 873 probe sets for genes that were differentially expressed between polyarticular JIA and controls. Hierarchical clustering of these probe sets distinguished three subgroups within polyarticular JIA. Prototypical subjects within each subgroup were identified and used to define subgroup-specific gene expression signatures. One of these signatures was associated with monocyte markers, another with transforming growth factor-beta-inducible genes, and a third with immediate-early genes. Correlation of these gene expression signatures with clinical and biological features of JIA subgroups suggests direct relevance to aspects of disease activity and supports the division of polyarticular JIA into distinct subsets. Conclusions. PBMC gene expression signatures in recent onset polyarticular JIA reflect discrete disease processes and offer a molecular classification of disease. Keywords: Patient vs. control, reassessment of phenotype
2009-06-30 | GSE13849 | GEO
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2016-06-24 | E-GEOD-80600 | biostudies-arrayexpress
Project description:cRNAs were hybridized with HumU133A oligo arrays (Affymetrix, Santa Clara, CA) which contain 22,283 probe sets. Preliminary studies indicated that Affymetrix Human GeneChips detected more than 60% of pig liver transcripts. All Affymetrix data were filtered for those genes with fluorescent intensity value of less than 100. Genes whose expressions in livers from the folate deficient and ethanol fed groups were either increased or decreased by 2-fold or more (p<0.05) compared to those in livers from the control group were considered significantly changed. GeneChip cRNA probes used in GeneChip expressions were obtained by following a protocol from the manufacturer. First strand cDNA was synthesized by reverse transcription of 8 μg total RNA with superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and T7-oligo (dT) 24 primer (Genset Oligos, Boulder, CO), followed by second strand cDNA synthesis. Biotin-labeled cRNA probes were generated by reverse transcription of double stranded cDNA using BioArray High yield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). The cRNA probes were purified from unincorporated nucleotides by RNeasy mini column (QIAGEN, Valencia, CA), fragmented and hybridized overnight at 680 C to the Human GeneChip array (HG U133A, Affymetrix). Keywords: parallel sample
2004-12-22 | GSE2099 | GEO
Project description:Analysis of gene expression in Ws-0 lec1 (LEAFY COTYLEDON1) mutant Arabidopsis thaliana. Developmental stages studied includes 24-Hr post-fertilization, globular stage, cotyledon stage, mature green stage, post-mature green stage, and seedlings. Microarray Methods: Total RNA was extracted using the Hot Borate Method [Stones et. al. PNAS vol 98 no 20: 11806-11811 (2001)]. Biotinylated cRNA were prepared using the ENZO BioArray High Yield RNA Transcript Labeling Kit (Farmingdale, NY). cRNA was subsequently hybridized to Affymetrix ATH1 Arabidopsis GeneChips. The scanned array images were analyzed using Affymetrix Microarray Suite 4.0 (MAS 4.0) with a global scaling intensity set at 500.
2008-06-11 | E-GEOD-1051 | biostudies-arrayexpress
Project description:Objective. To identify gene expression differences in peripheral blood from patients with early and late onset juvenile idiopathic arthritis (JIA). Methods. Peripheral blood mononuclear cells (PBMC) were isolated from 56 healthy controls and 104 patients with recent onset JIA (39 persistent oligoarticular, 45 RF-polyarticular, and 20 systemic). Poly(A) RNA was amplified and labeled using NuGEN Ovation, and gene expression assessed with Affymetrix HG-U133 Plus 2.0 GeneChips®. Results. A total of 832 probe sets revealed gene expression differences (false-discovery rate 5%) in PBMC from children with oligoarticular JIA whose disease began before 6 years of age (age at onset [AaO] <6; early onset), compared to subjects whose disease began at 6 years of age or later (AaO ?6; late onset). In early onset patients there was greater expression of genes related to B-cells, and lesser expression of genes related to cells of the myeloid lineage. Support Vector Machine algorithms identified samples from early or late onset oligoarticular (97% accuracy) or polyarticular (89% accuracy) JIA patients, but not systemic JIA patients or healthy controls. Principal component analysis showed that the major classifier of samples was AaO regardless of whether they had oligoarticular or polyarticular JIA. Conclusion. PBMC gene expression analysis reveals biologic differences between early and late onset JIA patients independent of classification based on the number of joints involved. These data suggest AaO may be an important parameter to consider in JIA classification. Furthermore, different pathologic mechanisms may influence AaO, and understanding these processes may lead to improved treatment of JIA. Methods. Peripheral blood mononuclear cells (PBMC) were isolated from 56 healthy controls and 104 patients with recent onset JIA (39 persistent oligoarticular, 45 RF-polyarticular, and 20 systemic). Poly(A) RNA was amplified and labeled using NuGEN Ovation, and gene expression assessed with Affymetrix HG-U133 Plus 2.0 GeneChips®.
2011-02-14 | E-GEOD-20307 | biostudies-arrayexpress
Project description:To understand consequences of loss of FSH receptor, we used genetically altered mouse mutants with deletion of this receptor. Follitropin Receptor Knockout (FORKO) mice present various developmental and age-dependent abnormalities such as infertility, senescence and increased tumor incidences in addition to other phenotypes. To explore why the atrophic ovaries of FORKO mice develop ovarian anomalies later in life, we used expression profiling studies to gain a more comprehensive view of genes that are misregulated. Experiment Overall Design: Mice were housed under controlled temperature and constant light (12 h of light, 12 h of darkness), with food and water provided ad libitum. The female mice used in this experiment were derived by breeding heterozygotes of the 129T2 svEmsJ background. Experiment Overall Design: For RNA extraction, both the ovaries from 8 month old mice were carefully dissected and pooled. Tissues were frozen in liquid nitrogen and homogenized in TRIZOL (Invitrogen, Burlington, Ontario) and processed in accordance with the manufacturerâs protocol. Experiment Overall Design: Affymetrix 39 K GeneChip® Mouse Genome 430 2.0 Array has over 45000 probe sets which analyses 39000+ transcripts and variants from over 34000 well characterized mouse genes. A total of 1 µg of double-stranded cDNA was transcribed in vitro using the Bioarray High-Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY) according to the manufacturer's instructions using biotinylated CTP and UTP (Enzo, Farmingdale, NY). Following 5-hr incubation at 37°C, the resultant biotin-labeled cRNA was purified with RNAeasy columns (Qiagen) and eluted in 40 µl of RNAse-free water. The concentration of biotin-labeled cRNA was determined by RNA bio-analyzer. Target cRNAs corresponding to either wild type ovary or FORKO ovarian tissue were hybridized to an individual GeneChip from an identical lot of Affymetrix 39 K GeneChip® Mouse Genome 430 2.0 array for 16 hr. GeneChip arrays were washed and stained using antibody-mediated signal amplification and the Affymetrix Fluidics Station's standard Eukaryotic GE Wash 2 protocol, using Affymetrix equipment and protocols (Affymetrix, Santa Clara, CA).
2008-06-13 | E-GEOD-4323 | biostudies-arrayexpress
Project description:We used high density oligonucleotide arrays to measure the relative expression levels of ~27,000 probe sets in the left ventricles of inbred rat strains; DA (high performing), Copenhagen (COP, low performing), as well as F1(COPxDA) rats bred from these two strains whose performance was intermediate relative to both parental strains. DA and COP rats differ for both intrinsic aerobic running capacity (assessed with a treadmill exercise test to exhaustion) and intrinsic cardiac performance (as assessed by the Langendorff-Neeley working heart model). Previous work also showed a strong correlation between intrinsic aerobic running capacity and intrinsic cardiac performance. The inbred rats were maintained under specific pathogen free conditions and had access to pelleted rat chow (diet #5001, Purina Mills, Richmond, IN) and water ad libitim. The rats were housed with a target room temperature and humidity of 22oC and 40%, respectively, and 12:12 hour light dark cycle,with the light cycle occurring in the daytime (6 A.M. – 6 P.M.). The aerobic running capacity of the rats used in this study was assessed using a single week of treadmill endurance running tests, occurring at 11 weeks of age, and the rats were allowed 4 weeks to recover. Rats were killed at 15 weeks of age and their left ventricles were dissected. RNA was isolated by homogenizing the left ventricles of the heart in an ice cold guanidine thiocyanate/phenol solution (Ultraspec, Biotecx Laboratories, Houston, TX), extracted with chloroform and isolated using RNA Tack Resin (Biotecx Laboratories). Total RNA was further purified by ethanol precipitation and absorption to a column (RNeasy, Qiagen, Valencia, CA). Double-stranded cDNA was synthesized from 15 micrograms total RNA from each rat (four rats per strain) using reverse transcriptase (SuperScript II, InVitrogen, Carlsbad, CA) and T7-(dT)24 as the oligonucleotide primer. Biotinylated cRNA was synthesized using a kit (Enzo Bioarray High Yield RNA transcript Labeling Kit, Enzo Diagnostics, Farmingdale, NY) according to the manufacturer’s instruction and cRNAs were purified on columns (RNeasy mini kit, Qiagen). Each cRNA was fragmented according to the protocol in the Affymetrix GeneChip Expression Analysis manual and their quality was assessed by hybridization of a 5 microgram aliquot to a test chip (TestChip3, Affymetrix). 15 micrograms of the probe was hybridized to each of a set of three rat GeneChips (U34A, B, and C; Affymetrix). Hybridization, washing, staining with streptavidin-phycoerythrin, and scanning were performed at the Medical College of Ohio Core Facility according to the manufacturer's (Affymetrix) instructions. Complete transcription and hybridization were validated with bacterial sequences as an external control and several housekeeping genes as an internal control. Absolute analysis of data were conducted using the default settings of the Affymetrix software (GeneChip Software MAS-5.0). Microarray images were scaled to an average hybridization intensity of 150 to normalize the signals between individual chips. Keywords = quantitative real-time RT-PCR Keywords = insulin receptor substrate 2 (Irs2) Keywords = phosphatidylinositol 3-kinase Keywords = regulatory subunit 1 Keywords = (Pik3r1) Keywords = endurance running Keywords = treadmill running Keywords: parallel sample
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