Ontology highlight
ABSTRACT:
PROVIDER: PRJNA705169 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13791830_1.fastq.gz | Fastqsanger.gz | |||
| SRR13791830_2.fastq.gz | Fastqsanger.gz | |||
| SRR13791831_1.fastq.gz | Fastqsanger.gz | |||
| SRR13791831_2.fastq.gz | Fastqsanger.gz | |||
| SRR13791832_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 56 |
Similar Datasets
Project description:By studying differently expressed immune genes with gene expression profiling in immune competent children researchers have been able to distinguish between children with asymptomatic viral infection and those with symptomatic viral infection as well as patients with bacterial infection. In this study we asked if gene expression profiling is feasible as a diagnostic tool in febrile neutropenia. We included children under treatment for a malignancy presenting with febrile neutropenia. Clinical data regarding the infectious episode was prospectively collected and children grouped based on microbiological agent detected into virus, bacteria, co-infection and unknown aetiology. Fourty three episodes had sufficient RNA for RNA-sequencing, 15 with respiratory tract virus, 22 with unknown etiology, 4 with co-infection and 2 with bacteria. No pathogen specific host-innate immune expression profile was seen in the group with virus, bacteria nor unknown aetiology probably due to the low white blood cell account (WBC). In the co-infection group with higher WBC but lower absolute neutrophil count (ANC) compared to the other groups, a downregulated innate response were detected. We conclude that gene expression profiling in children presenting with neutropenic fever is not a feasible diagnostic tool for febrile neutropenia in children with cancer due the low WBC.:
2020-08-26 | GSE152341 | GEO
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip
2011-12-31 | GSE28142 | GEO
Project description:This study aimed to use pan-viral detection microarrays to identify viruses in serum from cases of acute pediatric febrile illness in a tropical setting. Patient clinical data and serum samples were collected between 2005 and 2009 as part of an ongoing pediatric dengue virus study at the Hospital Infantil Manuel de Jesús Rivera in Managua, Nicaragua. This study focused on patients who presented with dengue-like illness but who tested negative for dengue-virus infection. We hypothesized that non-dengue viruses or previously uncharacterized viruses might be causing these illnesses. The Virochip microarray is capable of detecting known viruses and discovering novel viruses. This series includes 153 arrays corresponding to 148 cases and 5 HeLa controls. Keywords: viral detection, tropical febrile illness, dengue virus, Nicaragua, Virochip From each serum sample, total nucleic acid was extracted and used to prepare a randomly-primed dsDNA library. These libraries were fluorescently labeled and hybrized to Virochip arrays.
2011-12-31 | E-GEOD-28142 | biostudies-arrayexpress
Project description:This randomized clinical trial studies prophylactic colony stimulating factor management in patients with breast, colorectal or non-small cell lung cancer receiving chemotherapy and with risk of developing febrile neutropenia. Patients receiving chemotherapy may develop febrile neutropenia. Febrile neutropenia is a condition that involves fever and a low number of neutrophils (a type of white blood cell) in the blood. Febrile neutropenia increases the risk of infection. Colony stimulating factors are medications sometimes given to patients receiving chemotherapy to prevent febrile neutropenia. Colony stimulating factors are given to patients based on guidelines. Some clinics have an automated system that helps doctors decide when to prescribe them when there is a high risk of developing febrile neutropenia. Gathering information about the use of an automated system to prescribe prophylactic colony stimulating factor may help doctors use colony stimulating factor when it is needed.
| 2211802 | ecrin-mdr-crc
Project description:Viral infections are among the most common causes for fever without an apparent source (FWS) in young children; however, many febrile children are treated with antibiotics despite the absence of bacterial infection. Adenovirus, human herpesvirus 6 (HHV-6) and enterovirus are detected in children with FWS more often than other viral species. Virus and bacteria interact with pattern recognition receptors in circulating blood leukocytes and trigger specific host transcriptional programs that mediate immune response, and unique transcriptional signatures may be ascertained to discriminate between viral and bacterial causes for children with FWS. Microarray analyses were conducted on peripheral blood samples obtained from 51 pediatric patients with confirmed adenovirus, human herpesvirus 6 (HHV-6), enterovirus or bacterial infection. Whole blood transcriptional profiles could clearly distinguish febrile children from healthy controls, and febrile children with viral infections from afebrile children carrying the same virus. Molecular pathways regulating host immune response were the most affected in febrile children with infection. Pattern recognition programs were prominently activated in all febrile children with infection, while differential activation of transcriptional programs was observed among viral species. Interferon signaling pathway was uniquely activated in children with febrile viral infection, while a different set of pathways was uniquely activated in children with bacterial infection. Transcriptional signatures were identified and classified febrile children with viral or bacterial infection with 87% overall accuracy, an improvement from the current clinical practice of deducing from white blood cell (WBC) count status. Similar degree of accuracy was observed when we validated the signature probes on data sets from an independent study with different microarray platforms. The current study confirms the clinical utility of blood transcriptional analysis, suggests the composition of transcriptional signatures which can be used to ascertain the infectious etiology of febrile young children without an apparent source, thus limit the overuse of antibiotics on febrile children presenting with this common clinical complaint. Total RNA samples extracted from whole blood of young children were processed for hybridization onto Illumina Human-HT12 version 4 beadchips, and differential expression of the transcripts was analyzed between sick children with either viral or bacterial infection and healthy children.
2012-10-15 | E-GEOD-40396 | biostudies-arrayexpress
Project description:We report a detailed characterization of the HPV16 genome in two brain metastases from OPSCC tumors. The use of a target enrichment strategy followed by next generation sequencing (NGS) provided an effective way to identify viral infection in tumor genome, including internal deletions and insertion sites into the host genome. Applying similar strategies to a larger cohort of HPV+ HNSCC brain metastases could help to identify biomarkers that can predict metastasis and/or identify novel therapeutic options.
2021-02-28 | MSV000086965 | MassIVE
Project description:Viral Detection Microarray Analysis of Unknown Tropical Febrile Illness Cases
| PRJNA139553 | ENA
Project description:Purpose: The goal of this study is to determine the expression profile of HHV-6B in whole blood samples from transplant patients with HHV-6B genomes detected in plasma Methods: Viral mRNA profiles in whole blood samples of different transplant patients were generated by deep sequencing using Illumina Hiseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation for U38 expression was performed using TaqMan Results: Hierarchical clustering uncovered systematic detection of U38 mRNA transcripts in whole blood samples from all patients with a detectable HHV-6B reactivation in their plasma Conclusions: Our study represents the first detailed analysis of viral transcriptomes associated with HHV-6B reactivation in whole blood samples generated by RNA-seq technology. Our results show that NGS offers a comprehensive and more accurate qualitative evaluation of mRNA content within a whole blood sample.
2018-09-08 | GSE115533 | GEO
Project description:In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides array Comparative Genomics Hybridization (aCGH, Agilent) , we used a commerical SNP-array (Illumina) including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.
2015-10-01 | GSE73190 | GEO