Ontology highlight
ABSTRACT:
PROVIDER: PRJNA949987 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24003989.fastq.gz | Fastqsanger.gz | |||
| SRR26883100.fastq.gz | Fastqsanger.gz | |||
| SRR26883101.fastq.gz | Fastqsanger.gz | |||
| SRR26883102.fastq.gz | Fastqsanger.gz | |||
| SRR26883103.fastq.gz | Fastqsanger.gz |
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Project description:Metegenomic sequencing of blood from patients with febrile neutropenia, and controls
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Project description:We have isolated extracellular vesicles from healthy donors' plasma, other febrile illness plasma, mild dengue patients (Platelet counts= >100,000 per mm3 of blood) , and severe dengue patients' plasma (Platelet counts= <30,000 per mm3 of blood) by ultracentrifugation. For understanding, the differences in protein cargo among the EVs isolated from these groups were subjected to SWATH analysis. We have used three biological replicates of each group of EVs. A- EVS DERIVED FROM SEVERE DENGUE PLASMA B- EVS DERIVED FROM MILD DENGUE PLASMA C- EVS DERIVED FROM OTHER FEBRILE ILLNESS PLASMA D- EVS DERIVED FROM HEALTHY DONORS PLASMA
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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.:
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Project description:RNA extracted from CD34+ isolated from Acute Myeloid Leukemia patients at the diagnosis and co-cultured with extracellular vesicles from plasma of AML patients at the diagnosis. Gene expression profiling was analyzed on the nCounter system using the Human Metabolic Pathways Panel comparing the expression profiles of EV-treated CD34+ cells and control (vehicle) CD34+ cells.
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Project description:ABSTRACT Background. Acute Kawasaki disease (KD) is difficult to distinguish from other acute rash/fever illnesses, in part because the etiologic agent(s) and pathophysiology remain poorly characterized. As a result, diagnosis and critical therapies may be delayed. Methods. We used DNA microarrays to identify possible diagnostic features of KD. We compared gene expression patterns in the blood of 23 children with acute KD and 18 age-matched febrile children with three illnesses that resemble KD. Results. Genes associated with platelet and neutrophil activation were expressed at higher levels in KD patients than in patients with acute adenovirus infections or systemic adverse drug reactions but not in patients with scarlet fever; genes associated with B cell activation were also expressed at higher levels in KD patients than in controls. A striking absence of interferon-stimulated gene expression in the KD patients was confirmed in an independent cohort of KD subjects. We successfully predicted the diagnosis in 21 of 23 KD patients and 7 of 8 adenovirus patients using a set of 38 gene transcripts. Conclusions. These findings provide insight into the molecular features that distinguish KD from other febrile illnesses, and support the feasibility of developing novel diagnostic reagents for KD based on the host response. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Disease State: One of Kawasaki Disease (KD) or control (C) of Scarlet fever (C-sf), adenovirus infection (C-ai) or drug reaction (C-dr) disease_state_design
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Project description:MicroRNAs are a family of 19- to 25-nucleotides noncoding small RNAs that primarily function as gene regulators. Aberrant microRNA expression has been described for several human malignancies, and this new class of small regulatory RNAs has both oncogenic and tumor suppressor functions. Despite this knowledge, there is little information regarding microRNAs in blood especially because microRNAs in blood, if exist, were thought to be digested by RNase. Recent studies, however, have revealed that microRNAs exist and escape digestion in serum and plasma. Thus, we performed microRNA microaray to obtain insight into microRNA deregulation in the plasma of a leukemia patient. Here, we have revealed that microRNA-638 (miR-638) is stably present in human plasmas, and miR-92a dramatically decreased in the plasmas of acute leukemia patients. Our data indicate that the ratio of miR-92a/miR-638 in plasma has strong potential for clinical application as a novel biomarker for detection of leukemia. Seven normal samples and two acute leukemia samples ware profiled and compared.
2010-05-16 | E-GEOD-14772 | biostudies-arrayexpress
Project description:ABSTRACT Background. Acute Kawasaki disease (KD) is difficult to distinguish from other acute rash/fever illnesses, in part because the etiologic agent(s) and pathophysiology remain poorly characterized. As a result, diagnosis and critical therapies may be delayed. Methods. We used DNA microarrays to identify possible diagnostic features of KD. We compared gene expression patterns in the blood of 23 children with acute KD and 18 age-matched febrile children with three illnesses that resemble KD. Results. Genes associated with platelet and neutrophil activation were expressed at higher levels in KD patients than in patients with acute adenovirus infections or systemic adverse drug reactions but not in patients with scarlet fever; genes associated with B cell activation were also expressed at higher levels in KD patients than in controls. A striking absence of interferon-stimulated gene expression in the KD patients was confirmed in an independent cohort of KD subjects. We successfully predicted the diagnosis in 21 of 23 KD patients and 7 of 8 adenovirus patients using a set of 38 gene transcripts. Conclusions. These findings provide insight into the molecular features that distinguish KD from other febrile illnesses, and support the feasibility of developing novel diagnostic reagents for KD based on the host response. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Disease State: One of Kawasaki Disease (KD) or control (C) of Scarlet fever (C-sf), adenovirus infection (C-ai) or drug reaction (C-dr)
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