RNA sequencing reveals differential long noncoding RNA expression profiles in bacterial and viral meningitis in children
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1043123 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26890800_1.fastq.gz | Fastqsanger.gz | |||
| SRR26890800_2.fastq.gz | Fastqsanger.gz | |||
| SRR26890786_1.fastq.gz | Fastqsanger.gz | |||
| SRR26890786_2.fastq.gz | Fastqsanger.gz | |||
| SRR26890787_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 30 |
Similar Datasets
Project description:1. Evaluate the diagnostic value of long noncoding RNA (CCAT1) expression by RT-PCR in peripheral blood in colorectal cancer patients versus normal healthy control personal.
2. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in diagnosis of colorectal cancer patients & its relation to tumor staging.
3. Evaluate the clinical utility of detecting long noncoding RNA (CCAT1) expression in precancerous colorectal diseases.
4. Compare long noncoding RNA (CCAT1) expression with traditional marker; carcinoembryonic antigen (CEA) and Carbohydrate antigen 19-9 (CA19-9) in diagnosis of colorectal cancer.
| 2330122 | ecrin-mdr-crc
Project description:The aim of the present study was to investigate the alteration of lncRNAs in bacterial and viral meningitis in children.The differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) were identified and the ceRNA network was characterized.
2023-11-21 | GSE248261 | GEO
Project description:BackgroundWe aimed to investigate the involvement of long non-coding RNA (lncRNA) in bacterial and viral meningitis in children.MethodsThe peripheral blood of five bacterial meningitis patients, five viral meningitis samples, and five healthy individuals were collected for RNA sequencing. Then, the differentially expressed lncRNA and mRNA were detected in bacterial meningitis vs. controls, viral meningitis vs. healthy samples, and bacterial vs. viral meningitis patients. Besides, co-expression and the competing endogenous RNA (ceRNA) networks were constructed. Receiver operating characteristic curve (ROC) analysis was performed.ResultsCompared with the control group, 2 lncRNAs and 32 mRNAs were identified in bacterial meningitis patients, and 115 lncRNAs and 54 mRNAs were detected in viral meningitis. Compared with bacterial meningitis, 165 lncRNAs and 765 mRNAs were identified in viral meningitis. 2 lncRNAs and 31 mRNAs were specific to bacterial meningitis, and 115 lncRNAs and 53 mRNAs were specific to viral meningitis. The function enrichment results indicated that these mRNAs were involved in innate immune response, inflammatory response, and immune system process. A total of 8 and 1401 co-expression relationships were respectively found in bacterial and viral meningitis groups. The ceRNA networks contained 1 lncRNA-mRNA pair and 4 miRNA-mRNA pairs in viral meningitis group. GPR68 and KIF5C, identified in bacterial meningitis co-expression analysis, had an area under the curve (AUC) of 1.00, while the AUC of OR52K2 and CCR5 is 0.883 and 0.698, respectively.ConclusionsOur research is the first to profile the lncRNAs in bacterial and viral meningitis in children and may provide new insight into understanding meningitis regulatory mechanisms.
| S-EPMC10863080 | biostudies-literature
Project description:Bacterial meningitis is usually fatal without treatment. Prompt and accurate diagnosis coupled with the timely administration of parenteral antibiotics is necessary in order to save lives. We used label-free mass spectrometry based quantitative proteomics to identify specific protein signatures in cerebrospinal fluid from Malawian children with Streptococcus pneumoniae infection, the leading cause of bacterial meningitis in children, elderly and people infected with Human Immunodeficiency Virus. Samples were analysed in two independent cohorts (cases and controls, n=12 for the discovery cohort and n=16 for the verification cohort). The protein profiles clearly discriminated cases and controls. Proteins involved in the immune response and exosome cell signaling were significantly enriched in the infected samples. Several S. pneumoniae membrane proteins were identified suggesting these as potential therapeutic targets. For both cohorts, over 200 human proteins were up and down-regulated in children with confirmed S. pneumoniae infection in comparison with controls. Compiling proteins up- and down- regulated in both discovery and verification cohorts, we generated a comprehensive list of over 140 proteins from which diagnostic biomarkers could be nominated. For a panel of five selected proteins (cathelicidin, ceruloplasmin, myeloperoxidase, cystatin C and protein S100A8/S100 A9), we additionally verified the label-free results by automated quantitative western blot immunoassays (Simple Western™), with excellent agreement between the two experimental approaches. The proteins identified in our study could form the basis of development of a biomarker panel for rapid diagnosis. Our results could lead to the development of point-of-care assays to inform diagnosis, and to nominate new targets for drugs and vaccines to improve disease management and consequently to enhance the prognosis of children with bacterial meningitis.
2017-08-03 | PXD004219 | Pride
Project description:Whole blood transcriptional profiles in children with or without tuberculous meningitis (TBM) were compared using RNA-Seq and a biomarker signature driven by inflammasome activation and signaling was identified
2019-08-06 | GSE111459 | GEO
Project description:Cerebrospinal fluid transcriptional profiles in children with tuberculous meningitis (TBM) or other infections were compared using RNA-Seq and a biomarker signature driven by NMDA-receptor activation was identified
2019-08-06 | GSE122377 | GEO
Project description:Bacterial meningitis is usually fatal without treatment and prompt and accurate diagnosis coupled with the timely administration of parenteral antibiotics, are necessary in order to save lives. The diagnosis can sometimes be delayed whilst samples are analysed in a laboratory using traditional methods of microscopy and antigen testing. The objective of our project is to define specific protein signatures in cerebrospinal fluid associated with Streptococcus pneumoniae infection which could lead to the development of assays or point-of-care devices to improve the speed and accuracy of diagnosis, and guide the clinicians in the treatment and prognosis of children with bacterial meningitis. The associated research paper is in preparation.
2014-07-22 | PXD000764 | Pride
Project description:Background: Meningitis can be caused by several viruses and bacteria. Identifying the causative pathogen as quickly as possible is crucial to initiate the most optimal therapy, as acute bacterial meningitis is associated with a significant morbidity and mortality. Bacterial meningitis requires antibiotics, as opposed to enteroviral meningitis, which only requires supportive therapy. Clinical presentation is usually not sufficient to differentiate between viral and bacterial meningitis, thereby necessitating cerebrospinal fluid (CSF) analysis by PCR and/or time-consuming bacterial cultures. However, collecting CSF in children is not always feasible and a rather invasive procedure. Methods: In 12 Belgian hospitals, we obtained acute blood samples from children with signs of meningitis (49 viral and 7 bacterial cases). (aged between 3 months and 16 years). After pathogen confirmation on CSF, the patient was asked to give a convalescent sample after recovery. 3’mRNA sequencing was performed to determine differentially expressed genes (DEGs) to create a host transcriptomic profile. Results: Enteroviral meningitis cases displayed the largest upregulated fold change enrichment in type I interferon production, response and signaling pathways. Patients with bacterial meningitis showed a significant upregulation of genes related to macrophage and neutrophil activation. We found several significantly DEGs between enteroviral and bacterial meningitis. Random forest classification showed that we were able to differentiate enteroviral from bacterial meningitis with an AUC of 0.982 on held-out samples. Conclusions: Enteroviral meningitis has an innate immunity signature with type 1 interferons as key players. Our classifier, based on blood host transcriptomic profiles of different meningitis cases, is a possible strong alternative for diagnosing enteroviral meningitis.
2019-06-27 | GSE133378 | GEO
Project description:In this study, we performed label-free based CSF quantitative proteomics to identify and analyze the differentially expressed proteins among bacterial meningitis, viral meningitis and hospital controls (children with benign intracranial hypertension). Compared with viral meningitis and hospital controls, we screened 135 differentially expressed proteins to distinguish bacterial meningitis from viral meningitis and controls. Among of them, 69 proteins as potential biomarkers for the diagnosis of bacterial meningitis, including both novel and previously reported candidate protein markers.
2022-05-20 | PXD026663 | Pride
Project description:noncoding RNAs (ncRNAs) are reported to play crucial roles in many physiological and biological processes. However, knowledge of ncRNAs in children with systemic lupus erythematosus (cSLE) remains limited. Therefore, we investigate the ncRNA expression profile of cSLE. Microarrays were performed to identify changes in ncRNA and mRNA expression between children with SLE and paired healthy children.
2018-02-10 | GSE110396 | GEO