E3e69ed5-a2f1-4c2c-8dc5-06f2de243995 - samples
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ABSTRACT:
PROVIDER: EGAD00001007867 | EGA |
REPOSITORIES: EGA
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Project description:Single-cell multi-omic profiling of COVID19 patients recruited from University College London. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors. Samples are pooled, with 4 donors per pool. Germ-line genotypes derived from previous single-cell RNA-sequencing are provided (VCF) to aid demultiplexing of single-cell and assignment to specific patient donor samples.
| EGAD00001007865 | EGA
Project description:Single-cell multi-omic profiling of healthy controls, asymptomatic and hosptial-admitted COVID19 patients recruited from Newcastle University hospitals. These data also include healthy control volunteers treated with IV-LPS as inflammatory controls. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors.
| EGAD00001007866 | EGA
Project description:Eighteen patients admitted to CSMC and diagnosed with COVID19 by RT-PCR were stratified into COVID19 mild/moderate, severe, and recovery groups (n=5-6/group). Venous blood was collected into EDTA coated tubes and centrifuged to separate plasma and buffy coat. Plasma was collected and frozen at -80C, and the buffy coat was collected into cryo-preservation media and frozen at -80C. Recovered cells are sorted for live-dead staining, then fixed with methanol. Fixed single cells were further captured using 10x chromium Next GEM 3 prime v3.1 kit. Two patients samples from the same group were mixed, captured and sequenced together.
2020-09-24 | GSE154567 | GEO
Project description:Objective: COVID19 is caused by the SARS-CoV-2 virus and has been associated with severe inflammation leading to organ dysfunction and mortality. Our aim was to profile the transcriptome in leukocytes from critically ill ICU patients positive for COVID19 vs. those negative for COVID19 to better understand the COVID19 associated host response. Design: Transcriptome profiling of buffy coat cells via ribonucleic acid sequencing (RNAseq) at the time of admission to the ICU. Setting: Tertiary care ICU and academic laboratory. Subjects: All patients admitted to the ICU suspected of being infected with SARS-CoV-2, using standardized hospital screening methodologies, had blood samples collected at the time of admission to the ICU. Interventions: None. Measurement and Main Results: Age- and sex-matched ICU patients that were either COVID19+ (PCR positive, 2 genes) or COVID19- (PCR negative) were enrolled. Cohorts were well-balanced with the exception that COVID19- patients had significantly higher total white blood cell counts and circulating neutrophils and COVID19+ patients were more likely to suffer bilateral pneumonia compared to COVID19- patients. Further, the mortality rate for this cohort of COVID19+ ICU patients was 29%. Transcriptional analysis revealed that when compared to COVID19- patients, the altered transcriptional responses of leukocytes in critically ill COVID19+ ICU patients appeared to be associated with multiple interrelated outcomes, including but not limited to robust interferon (IFN)-associated transcriptional responses, a marked decrease in the transcriptional activity of genes contributing to protein synthesis and the dysregulated expression of genes that contribute to coagulation, platelet activation, Toll-like receptor activation, neurotrophin signaling, and protein SUMOylation/ubiquitination. Conclusions: COVID19+ patients on day 1 of admission to the ICU display a unique leukocyte transcriptional profile that distinguishes them from COVID19- patients. Identification of this profile provides guidance for future targeted studies exploring novel prognostic/therapeutic aspects of COVID19.
2020-10-01 | GSE154998 | GEO
Project description:Motivation Recently, single-cell DNA sequencing (scDNA-seq) and multi-modal profiling with the addition of cell-surface antibodies (scDAb-seq) have provided key insights into cancer heterogeneity. Scaling these technologies across large patient cohorts, however, is frequently cost and time prohibitive. Multiplexing, in which cells from unique patients and pooled into a single experiment, offers a possible solution. While multiplexing methods are available for scRNAseq, accurate demultiplexing in scDNAseq remains an unmet need. Results Here, we introduce SNACS: Single-Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting. SNACS relies on a combination of patient-level cell-surface identifiers and natural variation in genetic polymorphisms to demultiplex scDNAseq data. We demonstrated the performance of SNACS on a dataset consisting of multi-sample experiments from patients with leukemia where we knew truth from single-sample experiments from the same patients. Relative to demultiplexing methods derived from the scRNAseq literature, SNACS offered superior accuracy. Availability Implementation SNACS is available at https://github.com/olshena/SNACS.
2024-02-09 | GSE255224 | GEO
Project description:Background and Objectives Recently accumulating evidence demonstrates the rare occurrence of COVID19 vaccination- induced inflammation in the central nervous system. However, the precise immune dysregulation related to the COVID19 vaccination-associated autoimmunity remains elusive. Here we report a case of COVID19 vaccination-associated encephalitis, where single-cell RNA sequencing (scRNA-seq) analysis identified a distinct myeloid cell population in the blood during the acute phase of the disease. Methods Peripheral blood mononuclear cells (PBMCs) were analyzed by scRNA-seq to clarify the cellular components of the patients at both the acute and remission phases of the disease. The data obtained were compared to those acquired from a healthy cohort. Results In this study, scRNA-seq analysis of PBMCs identified a distinct myeloid cell population observed at the acute phase of encephalitis. The specific myeloid population was not detected both at the remission phase of the disease and the samples fromof a healthy cohort. Discussion Our findings illustrate the induction of a unique myeloid subset in COVID19 vaccination-associated encephalitis. Further accumulation of reports investigating the dysregulated immune signature of COVID19 vaccination-associated autoimmunity is warranted to clarify the pathogenic role of the myeloid subset observed in our study.
2023-02-20 | GSE205607 | GEO
Project description:Background and Objectives Recently accumulating evidence demonstrates the rare occurrence of COVID19 vaccination- induced inflammation in the central nervous system. However, the precise immune dysregulation related to the COVID19 vaccination-associated autoimmunity remains elusive. Here we report a case of COVID19 vaccination-associated encephalitis, where single-cell RNA sequencing (scRNA-seq) analysis identified a distinct myeloid cell population in the blood during the acute phase of the disease. Methods Peripheral blood mononuclear cells (PBMCs) were analyzed by scRNA-seq to clarify the cellular components of the patients at both the acute and remission phases of the disease. The data obtained were compared to those acquired from a healthy cohort. Results In this study, scRNA-seq analysis of PBMCs identified a distinct myeloid cell population observed at the acute phase of encephalitis. The specific myeloid population was not detected both at the remission phase of the disease and the samples fromof a healthy cohort. Discussion Our findings illustrate the induction of a unique myeloid subset in COVID19 vaccination-associated encephalitis. Further accumulation of reports investigating the dysregulated immune signature of COVID19 vaccination-associated autoimmunity is warranted to clarify the pathogenic role of the myeloid subset observed in our study.
2023-02-20 | GSE205606 | GEO
Project description:In order to investigate variations in the endotype of COVID19 patients, we completed an integrated analysis of 112 research participants, including 74 COVID19 patients versus 37 SARS-CoV-2 negative controls. COVID19 patients tested positive for SARS-CoV-2 infection by PCR and/or antibody testing and were hospitalized due to COVID19 symptoms, but none of them had developed severe pathology requiring ICU admission at the time of blood collection. The control group was recruited from the same hospital system but tested negative for SARS-CoV-2 infection. Research blood draws were obtained from consented participants and analyzed by matched SARS-CoV-2 seroconversion assays, plasma proteomics using two alternative platforms [mass-spectrometry (MS), and SOMAscan assays], 82-plex cytokine profiling using Meso Scale Discovery (MSD) assays, and immune cell profiling via mass cytometry (MC).
2021-03-04 | PXD022817 | Pride
Project description:Single cell RNAseq reveal covid19 vaccine response difference
| PRJNA818538 | ENA
Project description:Single cell RNAseq reveal covid19 patient immune response
| PRJNA646704 | ENA