Whole blood transcriptome from Covid-19 patients in India
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA807370 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:High throughput sequencing is performed on mRNA isolated from whole blood of adult Covid-19 patients, bacterial coinfection with Covid-19 and healthy controls in a South Indian cohort. Samples were collected from individuals at the time of hospitalization or visit to clinic. The Covid-19 samples are categorized by severeity.
2022-02-22 | GSE196822 | GEO
Project description:Red blood cells (RBC) depleted whole blood from COVID-19 patients and controls was harvested and processed in order to performed 10X single cell RNA-seq. For COVID-19 patients 2 samples 10 days a part were analyzed.
2020-08-21 | E-MTAB-9221 | biostudies-arrayexpress
Project description:Infection with SARS-CoV-2 has highly variable clinical manifestations, ranging from asymptomatic infection through to life-threatening disease. Host whole blood transcriptomics can offer unique insights into the biological processes underpinning infection and disease, as well as severity. We performed whole blood RNA-Sequencing of individuals with varying degrees of COVID-19 severity. We used differential expression analysis and pathway enrichment analysis to explore how the blood transcriptome differs between individuals with mild, moderate, and severe COVID-19, performing pairwise comparisons between groups.
2022-07-19 | E-MTAB-10926 | biostudies-arrayexpress
Project description:<p><strong>INTRODUCTION:</strong> COVID-19 has become a global impediment by bringing everything to a halt starting from January 2020. India underwent the lockdown starting from 22nd March 2020 with the sudden spike in the number of COVID-19 patients in major cities and states. This study focused on how metabolites play a crucial role in SARSCoV-2 prognosis.</p><p><strong>MATERIALS AND METHODS:</strong> Metabolome profiling of 106 plasma samples and 24 swab samples from symptomatic patients in the Indian population of the Mumbai region was done. COVID-19 positive samples were further segregated under the non-severe COVID-19 and severe COVID-19 patient cohort for both plasma and swab.</p><p><strong>RESULTS:</strong> After analyzing the raw files, total 7,949 and 12,871 metabolites in plasma and swab were found. 11 and 35 significantly altered metabolites were found in COVID-19 positive compared to COVID-19 negative plasma and swab samples, respectively. Also, 9 and 23 significantly altered metabolites were found in severe COVID-19 positive to non-severe COVID-19 positive plasma and swab samples, respectively. The majorly affected pathways in COVID-19 patients were found to be the amino acid metabolism pathway, sphingosine metabolism pathway, and bile salt metabolism pathway.</p><p><strong>CONCLUSION:</strong> This study facilitates identification of potential metabolite-based biomarker candidates for rapid diagnosis and prognosis for clinical applications.</p><p><br></p><p><strong>Blood plasma assay</strong> is reported in the current study <strong>MTBLS2291</strong>.</p><p><strong>Nasopharyngeal swab assay</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS2349' rel='noopener noreferrer' target='_blank'><strong>MTBLS2349</strong></a>.</p>
2022-01-13 | MTBLS2291 | MetaboLights
Project description:The coronavirus pandemic (COVID-19) is associated with secondary bacterial and fungal infections globally. In India, inappropriate use of glucocorticoids, high prevalence of diabetes mellitus and a conducive environment for fungal growth are considered as the main factors for increased incidence of COVID-19 associated mucormycosis (CAM). Few cases of CAM without steroid abuse and normal blood glucose levels were also reported during the pandemic. This study was designed to explore whether altered immune responses due to severe COVID-19 infection predisposes towards development of mucormycosis. The global transcriptome profiling of monocytes and granulocytic cells derived from CAM, Mucormycosis, COVID-19 and healthy control groups were performed to identify the differentially expressed genes (DEGs) involved in dysregulated host immune response towards respective diseased and healthy conditions.
2024-02-09 | GSE226677 | GEO
Project description:Understanding the process of immune remodeling and regulation in SARS-CoV-2 infected patients from hospitalization to rehabilitation is crucial for therapy of patients with COVID-19. Here, we performed a longitudinal whole-transcriptome RNA sequencing on peripheral blood mononuclear cell (PBMC) samples of 18 patients with mild, moderate or severe COVID-19 symptoms during the treatment, convalescence and rehabilitation stages. After identifying the differentially expressed mRNAs, miRNAs and lncRNAs between different clinical stages or different clinical types and predicting the target genes of non-coding RNAs, we analyzed the functional and regulatory networks of their interactions. The type I interferon response was found to be significantly down-regulated after the patient rehabilitation, and the humoral immunity declined rapidly from the convalescence stage. Robust T-cell activation and differentiation at the whole transcriptome level constituted the main events during the recovery process of COVID-19. The formation of this T cell immune memory had the characteristics of multi-directional and multi-level regulation, and presented a higher early differentiation in mild patients. These findings uncovered the dynamic pattern of immune responses and indicated the key role of T cell immunity in the formation of immune protection against COVID-19.
2020-11-23 | GSE157859 | 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:Dexamethasone improves the survival of COVID-19 patients in need of supplemental oxygen therapy. Hospitalized COVID-19 patients eligible for dexamethasone therapy were recruited from the general care ward in several centers in Greece and the Netherlands and whole blood transcriptomic analysis was performed before and after starting dexamethasone treatment. Peripheral blood mononuclear cells (PBMCs) were isolated from healthy individuals and COVID-19 patients and stimulated with inactivated SARS-CoV-2 ex vivo in the presence or absence of dexamethasone and their transcriptome was assessed.
2023-07-26 | GSE227585 | GEO
Project description:<p><strong>INTRODUCTION:</strong> COVID-19 has become a global impediment by bringing everything to a halt starting from January 2020. India underwent the lockdown starting from 22nd March 2020 with the sudden spike in the number of COVID-19 patients in major cities and states. This study focused on how metabolites play a crucial role in SARSCoV-2 prognosis.</p><p><strong>MATERIALS AND METHODS:</strong> Metabolome profiling of 106 plasma samples and 24 swab samples from symptomatic patients in the Indian population of the Mumbai region was done. COVID-19 positive samples were further segregated under the non-severe COVID-19 and severe COVID-19 patient cohort for both plasma and swab.</p><p><strong>RESULTS:</strong> After analyzing the raw files, total 7,949 and 12,871 metabolites in plasma and swab were found. 11 and 35 significantly altered metabolites were found in COVID-19 positive compared to COVID-19 negative plasma and swab samples, respectively. Also, 9 and 23 significantly altered metabolites were found in severe COVID-19 positive to non-severe COVID-19 positive plasma and swab samples, respectively. The majorly affected pathways in COVID-19 patients were found to be the amino acid metabolism pathway, sphingosine metabolism pathway, and bile salt metabolism pathway.</p><p><strong>CONCLUSION:</strong> This study facilitates identification of potential metabolite-based biomarker candidates for rapid diagnosis and prognosis for clinical applications.</p><p><br></p><p><strong>Nasopharyngeal swab assay</strong> is reported in the current study <strong>MTBLS2349</strong>.</p><p><strong>Blood plasma assay</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS2291' rel='noopener noreferrer' target='_blank'><strong>MTBLS2291</strong></a>.</p>
2022-01-13 | MTBLS2349 | MetaboLights
Project description:The identification of COVID-19 patients with high-risk of severe disease is a challenge in routine care. We performed blood RNA-seq gene expression analyses in severe hospitalized patients compared to healthy donors. Supervised and unsupervised analyses revealed a high abundance of CD177, a specific neutrophil activation marker, contributing to the clustering of severe patients. Gene abundance correlated with high serum levels of CD177 in severe patients. These results highlight neutrophil activation as a hallmark of severe disease and CD177 assessment as a reliable prognostic marker for routine care.
2021-05-27 | GSE171110 | GEO