Time-dependent changes in gene expression after endotoxinic challenge followed by LR12-scrambled or LR12 treatment.
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ABSTRACT: Gene expression assessment in blood from male Cynomolgus monkey after endotoxin challenge followed by intravenous infusion with peptide control (LR12-scrambled) or LR12. The samples were analyzed at different time-points: 0, 2, 4 and 8 hours 56 samples : 4 time points, 4 vehicle samples/time point, 4 peptide control samples/time point, 6 LR12 samples/time point
Project description:Gene expression assessment in blood from male Cynomolgus monkey after endotoxin challenge followed by intravenous infusion with peptide control (LR12-scrambled) or LR12. The samples were analyzed at different time-points: 0, 2, 4 and 8 hours
Project description:Identifying novel candidate biomarker gene differentially expressed in the peripheral blood cells of patients with early stage acute myocardial infarction using microarray as a high throughput screening technology. In this study, we used exon array profiling to investigate biomarker gene analyzing 49 patients samples (six time points) and 6 control samples. Whole-blood cell drawn from an antecubital vein at six time points following STEMI diagnosis. The first time (T0) was on patient admission to the Emergency Unit prior to receiving any medication. The second time (T2) blood collection occurred after successful mechanical reperfusion and stenting of the infarct artery within 2 h after T0. Collections for the subsequent four time points were at 12 h (T12), 24 h (T24), 36 h (T36) and 48 h (T48). For the control group, peripheral blood was collected at one time point.
Project description:The purpose of the study was to assess the patterns of global gene expression in peripheral blood cells before and at three time points after the administration of a trivalent influenza vaccine in human male subjects, and to relate these to the antibody response to the vaccine. The antibody titer data for these subjects is provided as a supplemental file. 119 healthy male human volunteers ages 19 - 41 years were recruited in the study. Whole-blood RNA samples were collected in PaxGene tubes before and at three time points after administration of a trivalent influenza vaccine. Baseline samples (before vaccination) are labeled as day 0. The three additional time points are days 1, 3, and 14 after vaccination. A total of 431 arrays, corresponding to 116 individuals, passed quality control and are included in this data set. These are distributed as follows: Day 0: 111 Samples Day 1: 110 Samples Day 3: 101 Samples Day 14: 109 Samples
Project description:The experiment was designed to generate a time series for epithelial model during development. Each time point had 3 replicates. The data set contained 5 time points over 10 days. They are day0, day3, day5,day7,day10.
Project description:To uncover new molecular mechanisms involved in IgAN pathogenesis, we compared the genomic profiles of 12 IgAN patients with 8 healthy subjects, We included addiotional disease controls 3 FSGS(Focal Segmenal glomerulosclerosis) patients and 3 membrano proliferative glomerulonephritis type I (MPGN-I) controls in our study to evaluate if the WNT-β-catenin and PI3K/Akt pathways were specfic to IgAN. Gene expression profile comparison between 12IgAN patients and 8 Healthy Subjects. Gene Set Enrichment Analysis (GSEA) performed on the additional disease controls determined that the a priori defined set of genes and the pathways generated were specific to the IgAN
Project description:We hypothesized that patients with sarcoidosis have characteristic mRNA profiles. Microarray analysis of gene expression was done on peripheral blood. Comparing peripheral blood from patients with sarcoidosis to controls, 872 transcripts were upregulated and 1039 were downregulated at >1.5-fold change and a significant q value. Several transcripts associated with interferon and STAT1 were upregulated. Lung and lymph node analyses also showed dramatic increases in STAT1 and STAT1-regulated chemokines. Granulomas in lymph nodes of patients with sarcoidosis expressed abundant STAT1 and phosphorylated STAT1. STAT1 might play an important role in sarcoidosis. This novel hypothesis unites seemingly disparate observations with regard to sarcoidosis including implication of a casual role for interferons, a suspected infectious trigger, TH1 predominating lymphocytes in bronchoalveolar lavage, and the association with hypercalcemia. This study tested the hypothesis that SpA is characterized by a distinct pattern of gene expression in peripheral blood of affected individuals compared with healthy controls. High-density, human GeneChip probe arrays were used to profile mRNA of peripheral blood cells from 18 subjects with SpA and 25 normal individuals. Samples were processed as two separate sets at different times. Blood samples were taken at a time when patients were not receiving systemic immunomodulatory therapy. Differential expression was defined as a 1.5-fold change with a q value <5%. Gene ontology and pathway information were also studied. Signals from 134 probe sets (representing 95 known and 12 unknown gene transcripts) were consistently different from controls in both Sets 1 and 2. Included among these were transcripts for a group of 20 genes, such as interleukin-1 receptors 1 and 2, NLRP2, SLPI, SPARC, and TREM-1 that are clearly related to the immune or inflammatory response and a group of 4 transcripts that have a strong role in bone remodeling. Our observations are the first to implicate SPARC, SLPI, and NLRP2, a component of the innate immune system, in the pathogenesis of SpA. Our results also indicate a possible role for interleukin-1 and its receptors in SpA. In accord with the bone pathology component of SpA, we also found that expression levels of transcripts reflecting bone remodeling factors are also distinguishable in peripheral blood from patients with SpA versus controls. These results confirm some previously identified biomarkers implicated in the pathogenesis of SpA and also point to novel mediators in this disease. Peripheral blood was collected from diseased and control subjects. The sarcoidosis portion of the study included 12 patients and 12 control subjects. The spondyloarthropathy study was done in two independent sets. The first set included 11 patients and the same 12 control subjects used for the sarcoidosis study. The second set included 7 patients and 13 control subjects. For each sample, total RNA was isolated and analyzed by hybridization on Affymetrix arrays.
Project description:The purpose of the study was to assess the patterns of global gene expression in peripheral blood cells before and at three time points after the administration of a trivalent influenza vaccine in human female subjects, and to relate these to the antibody response to the vaccine 128 healthy female human volunteers ages 19 - 41 years were recruited in the study. Whole-blood RNA samples were collected in PaxGene tubes before and at three time points after administration of a trivalent influenza vaccine. Baseline samples (before vaccination) are labeled as day 0. The three additional time points are days 1, 3, and 14 after vaccination. A total of 417 arrays, corresponding to 110 individuals, passed quality control, corresponded to individuals where at least two of the four arrays in the series were available, and corresponded to individuals who were ethnically homogeneous as determined by identity-by-state and multidimensional scaling analysis of their genotype data. That set of 417 arrays was used for analysis in the associated publication and was therefore included in this GEO upload. These are distributed as follows: Day 0: 107 Samples Day 1: 107 Samples Day 3: 105 Samples Day 14: 98 Samples
Project description:Gene expression was profiled in peripheral blood samples collected over three time points from patients during acute anaphylaxis and from healthy controls. Patients presented to the Emergency Department (ED) at Royal Perth Hospital with acute, moderately severe anaphylaxis. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2). The study design consisted of 12 subjects, 3 time points, and 2 clinical states (acute anaphylaxis, healthy controls).
Project description:Exposure to Persistant Organic Pollutants (POPs) is known to cause serious health effects in human but the gene expression profiles leading to development of differnet diseases and disorders are not fully understood. The knowledge of global gene expression will help us to devlop early disease or disorder biomarkers for POP induced health effects. We used microarrays to detail the global gene expression profile underlying the effects of high POP exposure to Slovak 45 month children leading to identification of distinct classes of up-regulated and down-regulated genes and cellular processes. High POP Exposed 45 month Slovak Children: Extraction of total RNA was performed by using Qiagen PAXgene Blood RNA Kit IVD according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microgram of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microgram of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HGU133 plus 2.0). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix GeneArray Scanner 3000. The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
Project description:Association of juvenile spondyloarthritis (jSpA) with the HLA-B27 genotype is well established, but there is little knowledge of other genetic factors with a role in disease development. The aim of the present study was to identify and confirm gene signatures and novel biomarkers in various cohorts of untreated and treated patients diagnosed with jSpA and other forms of juvenile idiopathic arthritis (JIA). DNA microarray gene expression was performed in 11 patients with jSpA and in four healthy controls, along with bioinformatics analysis of retrieved data (DAVID, GSEA, IPA). Total RNA was isolated from whole blood of 45 children with known HLA genotype and diagnosis of jSpA according to ILAR criteria, 11 children with oligo- and polyarticular forms of JIA, as well as 12 age and sex matched control participants without diagnosis of chronic inflammatory disease. Of those 11 patient and 4 controls were utilized in the microarrays experiments, while the rest were used in the follow-up qPCR analyses