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ABSTRACT:
PROVIDER: PRJNA1059147 | ENA |
REPOSITORIES: ENA
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Project description:Diagnostic value of Metagenomics Next Generation Sequencing in intracranial infection caused by mucormycosis
| PRJEB43821 | ENA
Project description:Purpose: Idenfication of microRNA biomarkers of Chronic wasting disease in serum from infected elk Methods: Illumina next generation was used to profile abundance of serum miRNA in elk naturally infected with chronic wasting disease and Hamsters experimentally infected with the 263K scrapie prion strains Results: A signature of 21 miRNAs with diagnostic potential was found to be altered in abundance in serum from CWD infected elk. Of these, 6 were similarily altered in the serum from the 263K infected hamsters Conclusion: These altered miRNA signatures may serve as the basis for non-invasive diagnostic assays for chronic wasting disease and may shed light on the pathogenesis of prion infection
2019-10-29 | GSE139501 | GEO
Project description:This retrospective multicenter pilot study aims to determine potential cell-free microRNAs (cfmiRs) that identify patients with primary GBM (pGBM) tumors and to monitor Glioblastoma (GBM) recurrence.
2023-05-26 | GSE184472 | GEO
Project description:To analyze the clinical factors affecting the positive rate of metagenomic next-generation sequencing (mNGS) in patients with spinal infection: A multicenter retrospective study
| PRJNA1014500 | ENA
Project description:Purpose: The goals of this study are to compare Next-generation sequencing (NGS)-derived transcriptome profiling (RNA-seq) in the lung of three tyeps of mice during influenza infection. Methods: Total RNA from lung was extracted using a modified TRIzol protocol and spectrophometrically quantitated. Library preparation and sequencing were conducted using 3’ inTAG next-generation sequencing . Differential gene expression for day 6 post influenza infection was determined relative to mock inoculated mice. Results: Differentially expressed genes were defined using p-value <0.01 and FDR-corrected p-value <0.1 cutoffs. We identified the transcripts in the lung of RIG-I-/-, MAVS -/- mice during influenza infection Our study represents the first detailed analysis of lung transcriptomes of Wild Type , RIG-I-/-, MAVS -/- mice during influenza infection , with biologic replicates, generated by RNA-seq technology.
2018-11-28 | GSE114232 | GEO
Project description:Background: Systemic inflammation is a whole body reaction that can have an infection-positive (i.e. sepsis) or infection-negative origin. It is important to distinguish between septic and non-septic presentations early and reliably, because this has significant therapeutic implications for critically ill patients. We hypothesized that a molecular classifier based on a small number of RNAs expressed in peripheral blood could be discovered that would: 1) determine which patients with systemic inflammation had sepsis; 2) be robust across independent patient cohorts; 3) be insensitive to disease severity; and 4) provide diagnostic utility. The overall goal of this study was to identify and validate such a molecular classifier. Methods and Findings: We conducted an observational, non-interventional study of adult patients recruited from tertiary intensive care units (ICU). Biomarker discovery was conducted with an Australian cohort (n = 105) consisting of sepsis patients and post -surgical patients with infection-negative systemic inflammation. Using this cohort, a four-gene classifier consisting of a combination of CEACAM4, LAMP1, PLA2G7 and PLAC8 RNA biomarkers was identified. This classifier, designated SeptiCyte® Lab, was externally validated using RT-qPCR and receiver operating characteristic (ROC) curve analysis in five cohorts (n = 345) from the Netherlands. Cohort 1 (n=59) consisted of unambiguous septic cases and infection-negative systemic inflammation controls; SeptiCyte® Lab gave an area under curve (AUC) of 0.96 (95% CI: 0.91-1.00). ROC analysis of a more heterogeneous group of patients (Cohorts 2-5; 249 patients after excluding 37 patients with infection likelihood possible) gave an AUC of 0.89 (95% CI: 0.85-0.93). Disease severity, as measured by Sequential Organ Failure Assessment (SOFA) score or the Acute Physiology and Chronic Health Evaluation (APACHE) IV score, was not a significant confounding variable. The diagnostic utility o f SeptiCyte® Lab was evaluated by comparison to various clinical and laboratory parameters that would be available to a clinician within 24 hours of ICU admission. SeptiCyte® Lab was significantly better at differentiating sepsis from infection-negative systemic inflammation than all tested parameters, both singly and in various logistic combinations. SeptiCyte® Lab more than halved the diagnostic error rate compared to PCT in all tested cohorts or cohort combinations. Conclusions: SeptiCyte® Lab is a rapid molecular assay that may be clinically useful in the management of ICU patients with systemic inflammation. SIRS and Sepsis ICU patients, admission samples Retrospective, mutli-site sutdy using retrospective physician adjudication as a comparator
2015-10-24 | E-GEOD-74224 | biostudies-arrayexpress
Project description:Consider the problem of designing a panel of complex biomarkers to predict a patient's health or disease state when one can pair his or her current test sample, called a target sample, with the patient's previously acquired healthy sample, called a reference sample. As contrasted to a population averaged reference, this reference sample is individualized. Automated predictor algorithms that compare and contrast the paired samples to each other could result in a new generation of test panels that compare to a person's healthy reference to enhance predictive accuracy. This study develops such an individualized predictor and illustrates the added value of including the healthy reference for design of predictive gene expression panels. The objective is to predict each subject's state of infection, e.g., neither exposed nor infected, exposed but not infected, pre-acute phase of infection, acute phase of infection, post-acute phase of infection. Using gene microarray data collected in a large-scale serially sampled respiratory virus challenge study, we quantify the diagnostic advantage of pairing a person's baseline reference with his or her target sample.
2016-06-22 | GSE73072 | GEO
Project description:F1 Arabidopsis thaliana plants from parents grown in absence/presence of acute/chronic Cr stress were analyzed in terms of Cr tolerance (evaluated by the half maximal effective concentration, EC50), germination, root length and hydroxide peroxide. F1 generation from parents grown in both acute and chronic stress showed significant higher levels of EC50 than F1 from unstressed parents. In addition, both F1 from Cr stressed parents showed quicker germination under Cr presence and F1 from parents cultivated under chronic stress displayed reduction of hydroxide peroxide levels under Cr stress compared to control. RNA-seq analyses were performed at 1 and 3 weeks after the beginning of stress at two levels of Cr excess for both generation (F0 and F1).
2022-09-28 | E-MTAB-11099 | biostudies-arrayexpress