Sepsis punctum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA765219 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20648455_1.fastq.gz | Fastqsanger.gz | |||
| SRR20648456_1.fastq.gz | Fastqsanger.gz | |||
| SRR20648457_1.fastq.gz | Fastqsanger.gz | |||
| SRR20648457_2.fastq.gz | Fastqsanger.gz | |||
| SRR20648458_1.fastq.gz | Fastqsanger.gz |
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Project description:The peripheral whole-blood transcriptome analysis has been used to the identification of biomarkers in different clinical syndromes. The ability to simultaneously measure the gene expression levels of the whole transcriptome is providing a broader view of clinical syndromes such as sepsis. The aim of this study was to assess the gene expression profiles of post-surgical patients with septic shock compared with patients without sepsis.
2014-03-15 | E-MTAB-1548 | biostudies-arrayexpress
Project description:Objective: It is unclear whether the host response of gram-positive sepsis differs from gram-negative sepsis at a transcriptome level. Using microarray technology, we compared the gene-expression profiles of gram-positive sepsis and gram-negative sepsis in critically ill patients. Design: A prospective cross-sectional study. Setting: A 20-bed general intensive care unit of a tertiary referral hospital. Patients: Seventy-two patients admitted to the intensive care unit. Interventions: Intravenous blood was collected for leukocyte separation and RNA extraction. Microarray experiements were then performed examing the expression level of 19,232 genes in each sample. Measurements and Main Results: There was no difference in the expression profile between gram-positive and gram-negative sepsis. The finding remained unchanged even when genes with lower expression level were included or after statistical stringency was lowered. There were, however, ninety-four genes differentially expressed between sepsis and control patients. These genes included those involved in immune regulation, inflammation and mitochondrial function. Hierarchical cluster analysis confirmed that the difference in gene expression profile existed between sepsis and control patients, but not between gram-positive and gram-negative patients. Conclusion: Gram-positive and gram-negative sepsis share a common host response at a transcriptome level. These findings support the hypothesis that the septic response is non-specific and is designed to provide a more general response that can be elicited by a wide range of different micro-organisms. Keywords: disease state analysis, gram-positive sepsis, gram-negative sepsis
2007-12-01 | GSE6535 | GEO
Project description:Objective: It is unclear whether the host response of gram-positive sepsis differs from gram-negative sepsis at a transcriptome level. Using microarray technology, we compared the gene-expression profiles of gram-positive sepsis and gram-negative sepsis in critically ill patients. Design: A prospective cross-sectional study. Setting: A 20-bed general intensive care unit of a tertiary referral hospital. Patients: Seventy-two patients admitted to the intensive care unit. Interventions: Intravenous blood was collected for leukocyte separation and RNA extraction. Microarray experiements were then performed examing the expression level of 19,232 genes in each sample. Measurements and Main Results: There was no difference in the expression profile between gram-positive and gram-negative sepsis. The finding remained unchanged even when genes with lower expression level were included or after statistical stringency was lowered. There were, however, ninety-four genes differentially expressed between sepsis and control patients. These genes included those involved in immune regulation, inflammation and mitochondrial function. Hierarchical cluster analysis confirmed that the difference in gene expression profile existed between sepsis and control patients, but not between gram-positive and gram-negative patients. Conclusion: Gram-positive and gram-negative sepsis share a common host response at a transcriptome level. These findings support the hypothesis that the septic response is non-specific and is designed to provide a more general response that can be elicited by a wide range of different micro-organisms. The study included seventy-two critically ill patients admitted to the intensive care unit (ICU) of Nepean Hospital, Sydney, Australia. Of these, fifty-five patients were diagnosed to have sepsis, as confirmed by microbiological culture. The remaining seventeen patients did not have sepsis and were therefore used as controls. The study was approved by the hospital ethics committee and informed consent was obtained from all patients or their relatives. Patient Samples. Whole blood was taken from each patient on admission to ICU. Neutrophils were separated from whole blood using density-gradient separation with Ficoll-PaqueP P(Amersham). Subsequent neutrophil RNA extraction was performed using guanidinium thiocyanate (Ambion). Microarray Experiment. The neutrophil RNA was converted to cDNA, fluorescently labeled and hybridized to its complimentary sequences on the microarray (Invitrogen). The fluorescent signals on each micrroarray were captured using the GenePix 4000B laser scanner (Axon Instruments). Expression level of each gene was represented by the intensity of its fluorescent signal. Data Extraction. All signal intensity values were processed using background-subtraction method. Prior to analysis, all values were log-transformed and normalized by fitting a print-tip group Lowess curve. Normalization minimizes bias due to dye chemistry, signal intensity or location of a gene on the array. It ensures the detection of genes that are truly differentially expressed, instead of those caused by experimental artifacts or variation in the hybridization process. After normalization, genes that had more than 50% of data missing were removed. We then selected genes that had at least 80% of the data showing two-fold changes from the geneâs median values. After filtering, 1617 genes were available for further analysis.
2010-05-25 | E-GEOD-6535 | biostudies-arrayexpress
Project description:Here we show that the Drosophila nuclear receptor DHR39 is necessary for male reproduction and acts as a global regulator of accessory gland gene expression. Mutants for the DHR39 transcription factor are sterile, with the majority of accessory gland genes expressed at reduced levels. Specific depletion of DHR39 within the accessory gland is sufficient to reduce male fecundity and accessory gland gene expression. Restoration of DHR39 in the accessory gland of DHR39 mutants rescues this sterility and transcriptional reduction. We conclude that DHR39 is a key regulator of most accessory gland genes, including ovulin and sex peptide, and is necessary for male fertility.
2021-01-01 | GSE159502 | GEO
Project description:The mortality risk from cancer-associated sepsis is differentially affected by individual cancer sites and host responses to sepsis are heterogenous. Native Hawaiians have a 2-fold higher mortality risk from cancer-associated sepsis than Whites and also higher mortality risk from colorectal cancer (CRC). We investigated this disparity by examining ethnic variation in the transcriptome of patients with CRC-associated sepsis and its relation to survival and genetic diversity. We conducted transcriptomic profiling of CRC tumors and adjacent non-tumor tissue obtained from adult patients of Native Hawaiian and Japanese ethnicity who died from cancer-associated sepsis. We examined differential gene expression in relation to patient survival and sepsis disease etiology.
2022-09-01 | GSE198103 | GEO
Project description:Sepsis is a severe clinical syndrome related to an exaggerated host immune response to infection as well as systematic inflammation and serious tissue damage. Sepsis-induced intestine injury is one of the most frequent and serious complications of sepsis. This study aimed to identify new mechanisms in sepsis-induced intestine injury through transcriptome profiling (RNA-seq).
2022-09-07 | GSE202261 | GEO
Project description:Sepsis is a syndromic response to infection and is frequently a final common pathway to death from many infectious diseases worldwide. The global burden of sepsis is difficult to ascertain, although a recent scientific publication estimated that there were 48.9 million cases and 11 million sepsis-related deaths worldwide, which accounted for almost 20% of all global deaths. Here we analyzed the whole blood transcriptome of 5 healthy controls and 5 patients with confirmed sepsis from the Department of Emergency, Division of Surgical critical care, Tongji Trauma Center, Tongji Hospital, Tongji Medical College. This research aims to understand the expression of immune cells in sepsis patients and to construct an immune cell landscape of sepsis.
2023-02-05 | GSE224095 | GEO
Project description:we conducted integrative multiple levels of omics data including transcriptome, phosphoproteome, proteome and metabolome in different time-course of sepsis-associated liver dysfunction (SALD). This is the first trial to suggest the statistical pathway of integrative multi-omics data in sepsis. Given the increasing number of studies collecting multi-omics data but limited overview of the methodological framework for integrative analyses (Liu, Ding et al. 2013, Petersen, Zeilinger et al. 2014, Shah, Bonder et al. 2015), integrative approach in sepsis with liver dysfunction in this study will provide novel insights into the development of sepsis and ultimately offer new tools for overcoming the present diagnostic limitation. Therefore, a combined multi-omics dataset will give better accessibility of adoption in disease, and insight to identify the promising candidates for therapeutic strategies.
2023-06-21 | PXD025800 | Pride
Project description:The temporal evolution of sepsis was monitored by transcriptional profiling of five critically ill children with meningococcal sepsis and sepsis-induced multiple organ failure. Blood was sampled at 6 time points during the first 48 hours of their admission to pediatric intensive care, where the children received standard clinical treatment including organ support and antimicrobial therapy. Striking transcript instability was observed over the 48 hours, with increasing numbers of regulated genes over time. Most notably, proposed biomarkers for sepsis risk stratification also showed expression instability, with varied expression levels over 48 hours. This study demonstrates the extent of the complexity of temporal changes in gene expression that occur during the evolution of sepsis-induced multiple organ failure. Importantly, stratification tools that propose expression of biomarkers must take into account the temporal changes, over the use of single snapshots that may be less informative.
2013-04-03 | E-MEXP-3850 | biostudies-arrayexpress
Project description:Although some studies reported the comprehensive mRNA expression analysis of coronavirus disease 2019 (COVID-19) using blood samples to understand its pathogenesis, the characteristics of RNA expression in COVID-19 and sepsis have not been compared. We compared the transcriptome expression of whole blood samples from patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patients with sepsis caused by other bacteria who entered the intensive care unit to clarify the COVID-19-specific RNA expression and understand its pathogenesis. Transcriptomes related to mitochondria were upregulated in COVID-19, whereas those related to neutrophils were upregulated in sepsis. However, the transcriptomes related to neutrophils were upregulated in both COVID-19 and sepsis compared to in healthy controls, whereas the mitochondrial transcriptomes were upregulated in COVID-19 and downregulated in sepsis compared to in healthy controls. Moreover, sepsis showed sub-optimal intrinsic apoptotic features compared with COVID-19. The transcriptome expression of COVID-19 has been examined in vitro but has not been widely validated using human specimens. This study improves the understanding of the pathogenesis of COVID-19 and can contribute to the development of treatments.
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