COVID-19 OR SARS-COV-2 - GEO DataSets

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Select item 2001558971.

Immunological Biomarkers of Fatal COVID-19: A Study of 868 Patients

(Submitter supplied) Information on the immunopathobiology of coronavirus disease 2019 (COVID-19) is rapidly increasing; however, there remains a need to identify immune features predictive of fatal outcome. This large-scale study characterized immune responses to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection using multidimensional flow cytometry, with the aim of identifying high-risk immune biomarkers. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
27 Samples

Download data: CNT

Series

Accession:: GSE155897

ID:: 200155897

SRA Run Selector

Select item 2001625622.

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community

(Submitter supplied) SARS-CoV-2 infection ranges from asymptomatic to severe with lingering symptomatology in some. This prompted investigation of whether or not asymptomatic disease results in measurable immune activation post-infection. Immune activation following asymptomatic SARS-CoV-2 infection was characterized through a comparative investigation of the immune cell transcriptomes from 43 asymptomatic seropositive and 52 highly exposed seronegative individuals from the same community four to six weeks following a superspreading event. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
108 Samples

Download data: TXT

Series

Accession:: GSE162562

ID:: 200162562

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001715243.

Columbia University/NYP COVID-19 Lung Atlas

(Submitter supplied) We profiled 116,314 cells using snRNA-seq of 20 frozen lungs obtained from 19 COVID-19 decedents and seven control patients with short postmortem interval (PMI) autopsies. The COVID-19 cohort comprises seven female and 12 male decedents, including 13 patients of Hispanic ethnicity, with an age range from 58 to >89 years who had acquired SARS-CoV-2 infection and succumbed to the disease. The average time from symptom onset to death was 27.5 days (range, 4–63 days). more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
27 Samples

Download data: CSV

Series

Accession:: GSE171524

ID:: 200171524

Select item 2001670754.

m6A modification in SARS-CoV-2 virus regulates host cell innate immune response

(Submitter supplied) It is urgent and important to understand the relationship of the widespread severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) with host immune response and study the underlying molecular mechanism. RNA modification landscape of SARS-CoV-2 and its functional relevance to host cell innate immune response remain unknown. N6-methylation of adenosine (m6A) in RNA regulates many physiological and disease processes. more...

Organism:: Chlorocebus aethiops; Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:: GPL29742 GPL29320
16 Samples

Download data: BEDGRAPH, BW, XLSX

Series

Accession:: GSE167075

ID:: 200167075

SRA Run Selector

Select item 2001595565.

scRNA-seq analysis of SARS-CoV-2 infected human islets

(Submitter supplied) Recent clinical data has suggestedsed a bi-directional relationship between Coronavirus disease 19 (COVID-19) and diabetes. Here, we showdemonstrateed the detection of SARS-CoV-2 in pancreatic endocrine cells in autopsy samples derived fromof COVID-19 patients. Single cell RNA-seq and immunostaining confirmed that multiple types of pancreatic islet cells can be infected byare susceptible to SARS-CoV-2, eliciting a cellular stress response and the induction of chemokines. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
5 Samples

Download data: MTX, TSV

Series

Accession:: GSE159556

ID:: 200159556

SRA Run Selector

Select item 2001643816.

Distinct B cell repertoires characterize patients with mild and severe COVID-19

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL24676
22 Samples

Download data: CSV, H5

Series

Accession:: GSE164381

ID:: 200164381

Analyze with GEO2R

Select item 2001643807.

Distinct B cell repertoires characterize patients with mild and severe COVID-19 [VDJ]

(Submitter supplied) Protective immunity against COVID-19 likely depends on the production of SARS-CoV-2 binding plasma cells and memory B cells after infection or vaccination. Previous work has shown evidence that germinal center reactions, a critical component of the B cell response, are disrupted in severe COVID-19. This may adversely affect protective immunity from re-infection. Consistent with an extrafollicular B cell response, severe COVID-19 patients have large scale changes in B cell populations such as elevated frequencies of clonally expanded, class switched, unmutated plasmablasts. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL24676
11 Samples

Download data: CSV

Series

Accession:: GSE164380

ID:: 200164380

Analyze with GEO2R SRA Run Selector

Select item 2001643798.

Distinct B cell repertoires characterize patients with mild and severe COVID-19 [GEX]

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
11 Samples

Download data: H5

Series

Accession:: GSE164379

ID:: 200164379

SRA Run Selector

Select item 2001664249.

Asymptomatic COVID-19: disease tolerance with efficient anti-viral immunity against SARS-CoV-2

(Submitter supplied) The immune responses and mechanisms limiting symptom progression in asymptomatic cases of SARS-CoV-2 infection remain unclear. We comprehensively characterized transcriptomic profiles, cytokine responses, neutralization capacity of antibodies and cellular immune phenotypes of asymptomatic patients with acute SARS-CoV-2 infection to identify potential protective mechanisms. Compared to symptomatic patients, asymptomatic patients had higher counts of mature neutrophils and lower proportion of CD169+ expressing monocytes in the peripheral blood. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20301
38 Samples

Download data: TXT

Series

Accession:: GSE166424

ID:: 200166424

SRA Run Selector

Select item 20015545410.

Whole blood transcriptome analysis reveals SARS-CoV-2 ORF8 as a potential therapeutic and vaccine target

(Submitter supplied) The open reading frame (ORF) 8 in severe acute respiratory syndrome coronaviruses (SARS-CoVs), associated with host adaptation and viral replication, is a hotspot for mutation. However, mutation effects on host immune responses remain unknown. Here, whole blood transcriptomics performed on patients infected with mutant SARS-CoV-2 (Δ382; 382-nt deletion in ORF8) show differing profiles from wildtype SARS-CoV-2. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20301
58 Samples

Download data: TXT

Series

Accession:: GSE155454

ID:: 200155454

SRA Run Selector

Select item 20017308311.

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

(Submitter supplied) Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop a new RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. more...

Organism:: Homo sapiens; synthetic construct

Type:: Other

Platforms:: GPL27609 GPL17769 GPL21697
70 Samples

Download data: RDAT, XLSX

Series

Accession:: GSE173083

ID:: 200173083

Analyze with GEO2R SRA Run Selector

Select item 20016166512.

JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells

(Submitter supplied) SARS-CoV-2 infection of human airway epithelium activates genetic programs leading to progressive hyperinflammation in COVID-19 patients. Here, we report on transcriptomes activated in primary airway cells by interferons and their suppression by Janus kinase (JAK) inhibitors. Deciphering the regulation of the angiotensin-converting enzyme 2 (ACE2), the receptor for SARS-CoV-2, is paramount for understanding the cell tropism of SARS-CoV-2 infection. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:: GPL21290
53 Samples

Download data: TDF, TXT

Series

Accession:: GSE161665

ID:: 200161665

PubMed Full text in PMC Similar studies

Select item 20016166413.

JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells (RNA-seq)

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21290
37 Samples

Download data: TXT

Series

Accession:: GSE161664

ID:: 200161664

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016166314.

JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells (ChIP-seq)

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21290
16 Samples

Download data: TDF

Series

Accession:: GSE161663

ID:: 200161663

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20017308615.

Developing RT-LAMP Assays for Detection of SARS-CoV-2 in Saliva

(Submitter supplied) Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a fast and convenient method to amplify and identify the transcripts of a targeted pathogen. We combined bioinformatic and experimental analyses to improve the RT-LAMP assay performance for COVID-19 diagnosis. First, we developed an improved algorithm to design LAMP primers targeting the nucleocapsid (N), membrane (M), and spike (S) genes of SARS-CoV-2. more...

Organism:: Homo sapiens; synthetic construct

Type:: Other

Platforms:: GPL22790 GPL26967
2 Samples

Download data: TXT

Series

Accession:: GSE173086

ID:: 200173086

Analyze with GEO2R SRA Run Selector

Select item 20017247116.

Predicting COVID-19 Severity with a Specific Nucleocapsid Antibody plus Disease Risk Factor Score

(Submitter supplied) Effective methods for predicting COVID-19 disease trajectories are urgently needed. Here, enzyme-linked immunosorbent assay (ELISA) and coronavirus antigen microarray (COVAM) analysis mapped antibody epitopes in the plasma of COVID-19 patients (n = 86) experiencing a wide range of disease states. The experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the intensive care unit (ICU), requirement for ventilators, or death. more...

Organism:: Human coronavirus 229E; Human respirovirus 3; Influenza A virus; Human coronavirus NL63; Severe acute respiratory syndrome-related coronavirus; Human coronavirus OC43; Human coronavirus HKU1; Severe acute respiratory syndrome coronavirus 2; Human parainfluenza virus 4b; Influenza B virus; Human respirovirus 1; Human metapneumovirus; Human respiratory syncytial virus B; Human adenovirus sp.; Homo sapiens; Human respiratory syncytial virus A; Dromedary camel coronavirus; Human orthorubulavirus 2

Type:: Protein profiling by protein array

Platform:: GPL30021
90 Samples

Download data: TXT

Series

Accession:: GSE172471

ID:: 200172471

Analyze with GEO2R

Select item 20016395917.

Transcriptome analysis of Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)-infected and Influenza A/H1N1-infected nasal turbinate and lung tissues

(Submitter supplied) We report the application of RNA sequencing for transcriptome analysis of SARS-CoV-2-infected and Influenza A-infected Human nasal turbinate and lung tissues, enabling the study of tissue responses to viral infections

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
48 Samples

Download data: XLSX

Series

Accession:: GSE163959

ID:: 200163959

SRA Run Selector

Select item 20015920118.

iPSC-derived Human Intestinal Organoids are permissive to SARS-CoV-2 infection

(Submitter supplied) We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using a directed differentiation protocol to generate mesenchyme free, regionally patterned intestinal organoids. These organoids were then infected with SARS-CoV-2, and sequencing was performed 1 and 4 days post infection

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
24 Samples

Download data: CSV

Series

Accession:: GSE159201

ID:: 200159201

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20016699019.

Modeling SARS-CoV-2 infection and its individual differences with ACE2-expressing human iPS cells

(Submitter supplied) Genetic differences are a primary reason for differences in the susceptibility and severity of COVID-19. Because iPS cells maintain the genetic information of the donor, they can be used to model individual differences in SARS-CoV-2 infection in vitro. We found that human iPS cells expressing the SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) (ACE2-iPS cells) can be infected with SARS-CoV-2. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
6 Samples

Download data: TXT

Series

Accession:: GSE166990

ID:: 200166990

SRA Run Selector

Select item 20016924120.

hPSC-derived cells to model Macrophage-mediated inflammation in COVID19 Hearts

(Submitter supplied) We systematically compared autopsy samples from non-COVID-19 donors and COVID-19 patients using RNA-seq and immunohistochemistry. We observed strikingly increased expression levels of CCL2 as well as macrophage infiltration in heart tissues of COVID-19 patients. We generated an immuno-cardiac co-culture platform containing human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) and macrophages. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
23 Samples

Download data: TXT, XLS, XLSX

Series

Accession:: GSE169241

ID:: 200169241

PubMed Similar studies SRA Run Selector

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