Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA966114 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25581837.fastq.gz | Fastqsanger.gz | |||
| SRR25581838.fastq.gz | Fastqsanger.gz | |||
| SRR25581839.fastq.gz | Fastqsanger.gz | |||
| SRR25581840.fastq.gz | Fastqsanger.gz | |||
| SRR25581841.fastq.gz | Fastqsanger.gz |
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Project description:The outbreak of coronavirus disease 2019 (COVID-19) is a global health emergency. Various omics results have been reported for COVID-19, but the molecular hallmarks of COVID-19, especially in those patients without comorbidities, have not been fully investigated. Here we collect blood samples from 231 COVID-19 patients, prefiltered to exclude those with selected comorbidities, yet with symptoms ranging from asymptomatic to critically ill. Using integrative analysis of genomic, transcriptomic, proteomic, metabolomic and lipidomic profiles, we report a trans-omics landscape for COVID-19. Our analyses find neutrophils heterogeneity between asymptomatic and critically ill patients. Meanwhile, neutrophils over-activation, arginine depletion and tryptophan metabolites accumulation correlate with T cell dysfunction in critical patients. Our multi-omics data and characterization of peripheral blood from COVID-19 patients may thus help provide clues regarding pathophysiology of and potential therapeutic strategies for COVID-19.
2021-10-06 | MTBLS2542 | MetaboLights
Project description:We found that histone H4 is a potential biomarker of COVID-19 pathogenesis. Bulk RNA-sequencing of endothelial cell samples from idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) patients as well as controls was used in addition to published sequencing data from peripheral blood mononuclear cells or bronchoalveolar lavage fluid cells from COVID-19 and IPF patients as well as controls.
2025-02-24 | GSE167410 | GEO
Project description:The objective of this experiment was to compare the transcriptomic profile (NanoString platform) of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients with mild disease, and patients with severe COVID-19 with and without dexamethasone treatment, and healthy controls. We analyzed PBMCs from 4 mild COVID patients, 3 severe COVID patients,4 severe COVID patients treated with dexamethasone, and 5 healthy controls
2023-03-23 | GSE227341 | GEO
Project description:Background: We previously identified a 50-gene signature that distinguished two groups of patients with increased risk of COVID-19 and IPF mortality. In this study we aimed to validate our previous findings and to study the source and trajectory of circulating immune cells expressing these 50 genes in patients with COVID19, post-COVID-19 Interstitial Lung Disease (ILD) and Idiopathic Pulmonary Fibrosis (IPF). Methods: Whole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 216 hospitalized patients with COVID-19, five patients with post-COVID-19-ILD, six patients with IPF and four controls from the University of South Florida (USF)/Tampa General Hospital (TGH). We measured the expression of the 50-gene signature using the nCounter analysis system (Nanostring), and the levels of Interleukin 6 (IL6), interferon γ-induced protein (IP10), Secreted Phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-β) in these patients by Luminex and Elisa tests. A 7-gene PCR assay was generated to validate the identification of COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Single Cell Controller (10X Genomics). For analysis of gene expression, we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger and Seurat packages. For statistical analysis, we used Kaplan-Meier survival curves, CoxPH models, Two-way ANOVA, T-test, Fisher’s exact and the Wilcoxon rank test. Results: We identified the presence of three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19. These risk groups had significant differences in IL6, IP10, SPP1 and TGFβ-1 levels. By applying scRNA-seq, we discovered a novel subtype of Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+ and high levels of the 7-gene signature. We denominated these cells as 7Gene-M-MDSC. These cells were not observed in survivors with post-COVID-19-ILD. The 43-gene signature was mostly expressed in naive CD4 T and memory CD4 T cells, Tregs, memory CD8 T GZMB+, memory CD8 T GZMK+ and naive CD8 T cells. While increased expression of genes in the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19 ILD, the expression of these genes remained low in IPF. Conclusion: A 50-gene, high-risk genomic profile in peripheral blood of COVID-19 can accurately predict COVID-19 mortality. This profile is characterized by a simultaneous increase in expression of seven genes originating from 7Gene-M-MDSCs and decreased expression of 43 genes originating primarily in T cell subsets. While increased expression of these 43 genes can be seen in survivors with post-COVID-19 ILD, their expression remains low in IPF.
2024-12-05 | GSE264196 | GEO
Project description:Rationale COVID-19 can cause ARDS, a life-threatening condition that requires long-term ventilation. Neutrophil activation is a key mediator of lung injury in ARDS. However, the relationship between peripheral neutrophil RNA expression at the time of severe illness and 28-day ventilator weaning has not yet been clarified. Objectives To clarify the relationship with 28-day ventilator weaning and whole blood RNA sequencing analysis in COVID-19 patients. Moreover, single-cell RNA-seq was performed on neutrophils to analyze changes in gene expression levels for each fraction. Methods Bulk sequencing was performed using whole blood from 28 COVID-19 ARDS patients (9 in the non-ventilator weaning group and 19 in the ventilator weaning group) and 16 healthy controls. Next, single-cell RNA-seq was performed on neutrophils isolated from peripheral blood of 5 COVID-19 ARDS patients (3 in the non-ventilator weaning group and 2 in the ventilator weaning group) and 6 healthy individuals. Measurements and Main Results Although there was no clear difference between the non-ventilator weaning group and the ventilator weaning group in bulk RNA-seq using whole blood, the result of single-cell RNA-seq revealed clear differences between the non-ventilator weaning group, the ventilator weaning group, and healthy individuals. Conclusions Our study suggests that gene expression in neutrophils at the time of severe illness in COVID-19 ARDS patients may be associated with 28-day ventilator weaning.
2025-12-04 | GSE234903 | GEO
Project description:Rationale COVID-19 can cause ARDS, a life-threatening condition that requires long-term ventilation. Neutrophil activation is a key mediator of lung injury in ARDS. However, the relationship between peripheral neutrophil RNA expression at the time of severe illness and 28-day ventilator weaning has not yet been clarified. Objectives To clarify the relationship with 28-day ventilator weaning and whole blood RNA sequencing analysis in COVID-19 patients. Moreover, single-cell RNA-seq was performed on neutrophils to analyze changes in gene expression levels for each fraction. Methods Bulk sequencing was performed using whole blood from 28 COVID-19 ARDS patients (9 in the non-ventilator weaning group and 19 in the ventilator weaning group) and 16 healthy controls. Next, single-cell RNA-seq was performed on neutrophils isolated from peripheral blood of 5 COVID-19 ARDS patients (3 in the non-ventilator weaning group and 2 in the ventilator weaning group) and 6 healthy individuals. Measurements and Main Results Although there was no clear difference between the non-ventilator weaning group and the ventilator weaning group in bulk RNA-seq using whole blood, the result of single-cell RNA-seq revealed clear differences between the non-ventilator weaning group, the ventilator weaning group, and healthy individuals. Conclusions Our study suggests that gene expression in neutrophils at the time of severe illness in COVID-19 ARDS patients may be associated with 28-day ventilator weaning.
2025-12-04 | GSE234902 | GEO
Project description:Transcriptomic profile of peripheral blood neutrophils in inflammatory bowel disease (Homo sapiens Raw sequence reads)
| PRJNA997815 | ENA
Project description:The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from patients with mild and severe COVID-19, as well as from non-infected healthy controls. Additionally, low-density granulocytes (LDGs) from patients with severe COVID-19 were included to understand their unique role. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in severe COVID-19 patients, contrasting with mild COVID-19 and healthy controls. LDGs from severe COVID-19 patients exhibited an immature neutrophil phenotype and lacked this IFN-I signature. These findings underscore the crucial role of neutrophil inflammasomes in driving inflammation during severe COVID-19. The study provides insights into the pathological mechanisms of severe COVID-19 and highlights potential targets for therapeutic intervention.
2024-07-23 | GSE272381 | GEO
Project description:Homo sapiens fresh whole blood was infected with Candida parapsilosis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Homo sapiens gene expression.
2018-12-26 | GSE114177 | GEO
Project description:Homo sapiens fresh whole blood was infected with Candida albicans SC5314. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2018-12-26 | GSE114174 | GEO