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Items: 1 to 20 of 708

1.

RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19 III

(Submitter supplied) Here we analyze the transcriptional profiles of homogenized lungs resected from young female APOE2, APOE3, and APOE4 knock-in mice on day 4 post infection with SARS-CoV-2 MA10. Weighted gene co-expression analysis identified gene modules enriched for genes implicated in T and B cell activation to be downregulated in APOE2 and APOE4 mice during COVID-19 progression.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
23 Samples
Download data: RDS, TSV
Series
Accession:
GSE200132
ID:
200200132
2.

scRNAseq of lungs from APOE knock-in mice with COVID-19

(Submitter supplied) We performed single cell RNA-sequencing of lungs from APOE knock-in mice in the absence of infection or four days post infection with SARS-CoV-2 MA10. Infected mice showed major remodeling of the cellular composition with expansion of myeloid cells and relative depletion of epithelial cells. In infected mice, APOE2 mice showed enrichment of pathways implicated in immune activation, consistent with immunologic misfiring.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
1 Sample
Download data: CSV, MTX, TSV, TXT
Series
Accession:
GSE199498
ID:
200199498
3.

RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
86 Samples
Download data
Series
Accession:
GSE184289
ID:
200184289
4.

RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19 II

(Submitter supplied) Here we analyze the transcriptional profiles of homogenized lungs resected from APOE2, APOE3, and APOE4 knock-in mice on day 4 post infection with SARS-CoV-2 MA10. This experiment validated a prior RNA-seq experiment revealing blunted adaptive immunity in APOE2 and APOE4 mice during COVID-19 progression.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
24 Samples
Download data: RDS, TSV
Series
Accession:
GSE184288
ID:
200184288
5.

RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19 I

(Submitter supplied) Here we analyze the transcriptional profiles of homogenized lungs resected from APOE2, APOE3, and APOE4 knock-in mice in the absence of infection (day 0) and on days 2 and 4 post infection with SARS-CoV-2 MA10. Weighted gene co-expression analysis identified gene modules enriched for genes implicated in T and B cell activation to be downregulated in APOE2 and APOE4 mice during COVID-19 progression.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
39 Samples
Download data: RDS, TSV
Series
Accession:
GSE184287
ID:
200184287
6.

TLR7 sensing of SARS-CoV-2 and IFN-I response by plasmacytoid dendritic cells leads to the hyperactivation of macrophages.

(Submitter supplied) To gain a comprehensive understanding of type I IFN or SARS-CoV-2 activated pDCs priming macrophages in regulating TLR4 meidated gene expression, we treated primary human blood monocytes with 30ng/ml IFNα or the supernatant of SARS-CoV-2 activated pDCs for 24 h and followed by 2 ng/ml LPS for 3 h. Cells were harvested and performed transcriptomic analysis via RNA-seq. We found that IFNα and supernatant of SARS-CoV-2 activated pDCs had similar effects on priming macrophages to induce massive inflammatory gene expression mediated by LPS.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
24 Samples
Download data: TSV
Series
Accession:
GSE182572
ID:
200182572
7.

Prevalence and Mechanisms of Mucus Plugging in COVID-19 Lung Disease

(Submitter supplied) Purpose: To investigate molecular mechanisms of SARS-CoV-2-induced mucin expression and synthesis and test candidate countermeasures. Methods: Bulk RNA-seq was performed on well-differentiated human bronchial epithelial (HBE) cell culture lysates with/without SARS-CoV-2 inoculation. Results: SARS-CoV-2-infected HBE cultures exhibited peak titers 3 days post inoculation, whereas induction of MUC5B/MUC5AC peaked 7-14 days post inoculation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
110 Samples
Download data: TXT
Series
Accession:
GSE210223
ID:
200210223
8.

ScRNA-seq analysis and functional characterization of myeloid lincRNAs differentially expressed during COVID-19

(Submitter supplied) Myeloid cell differentiation and immune-activation is controlled by numerous regulators, keeping the activity of the immune system within tight physiological limits. The transcriptional circuitries governing human myeloid immunity during COVID-19, however, remain incompletely understood. Recently, long non-coding RNAs were found to play important roles in immune gene regulation. Here, we studied human myeloid lineage specific lncRNAs by bulk and single cell RNA-seq and identified PIRAT (a.k.a. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL18573 GPL18460
15 Samples
Download data: TXT
Series
Accession:
GSE142503
ID:
200142503
9.

Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL24247 GPL16417
18 Samples
Download data
Series
Accession:
GSE189794
ID:
200189794
10.

Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection [RNA-Seq]

(Submitter supplied) The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Here we define multiple pathways by which the gut microbiome protects mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
6 Samples
Download data: XLSX
Series
Accession:
GSE189792
ID:
200189792
11.

Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection [16S rRNA]

(Submitter supplied) The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Via 16S sequencing of antibiotic-treated mice, we found that Clostridia species protect mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL16417
12 Samples
Download data: XLSX
12.

Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures

(Submitter supplied) The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). A better definition of the pulmonary host response to SARS-CoV-2 infection is required to understand viral pathogenesis and to validate putative COVID-19 biomarkers that have been proposed in clinical studies. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL24676
61 Samples
Download data: CSV, DCC, PKC
Series
Accession:
GSE209537
ID:
200209537
13.

Antibody from Single Human VH-rearranging Mouse Potently Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion

(Submitter supplied) Here, we describe a mouse model in which the primary B cell receptor (BCR) repertoire is generated solely through V(D)J recombination of a human VH1-2 heavy chain (HC) and, substantially, a human Vk1-33 light chain (LC). Thus, primary humanized BCR repertoire diversity in these mice derives from immensely diverse HC and LC antigen-contact complementarity-region-3 (CDR3) sequences generated de novo by non-templated junctional modifications during V(D)J recombination. more...
Organism:
Mus musculus
Type:
Other
Platforms:
GPL19057 GPL21626 GPL16417
15 Samples
Download data: TXT, XLS
Series
Accession:
GSE197255
ID:
200197255
14.

Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2

(Submitter supplied) Why individuals with Down Syndrome (DS, trisomy 21) are particularly susceptible to SARS-CoV-2 induced disease remains largely unclear. The choroid plexus secrets the cerebrospinal fluid and strongly expresses the ACE2 receptor and the chromosome 21 encoded TMPRSS2 protease. To investigate the role of the choroid plexus in SARS-CoV-2 central nervous system infection in DS, we established a new type of brain organoid from DS and isogenic euploid control iPSC that consists of a core of appropriately patterned functional cortical neuronal cell types that is surrounded by a patent and functional choroid plexus (CPCOs). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
9 Samples
Download data: XLS
Series
Accession:
GSE208575
ID:
200208575
15.

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

(Submitter supplied) Numerous host factors of SARS-CoV-2 have been identified by screening approaches, but delineating their molecular roles during infection and whether they can be targeted for antiviral intervention remains a challenge. Here we use Perturb-seq, a single-cell CRISPR screening approach, to investigate how CRISPR interference of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. more...
Organism:
Homo sapiens; Severe acute respiratory syndrome coronavirus 2; synthetic construct
Type:
Other
Platforms:
GPL29320 GPL26526
2 Samples
Download data
Series
Accession:
GSE208240
ID:
200208240
16.

Gene expression profile at single cell level of stromal vascular cells (SVC) from the subcutaneous adipose tissue (SAT) and the visceral adipose tissue (VAT) post-exposure to SARS-CoV-2 or mock conditions in vitro

(Submitter supplied) Obesity, characterized by chronic low-grade inflammation of the adipose tissue, is associated with adverse coronavirus disease 2019 (COVID-19) outcomes, yet the underlying mechanism is unknown. To explore whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of adipose tissue contributes to pathogenesis, we evaluated COVID-19 autopsy cases and deeply profiled the response of adipose tissue to SARS-CoV-2 infection in vitro.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
24 Samples
Download data: TAR
Series
Accession:
GSE208034
ID:
200208034
17.

Genome-wide transcriptome analysis of SARS-CoV-2 positive patients' mucosa, compared with negative controls.

(Submitter supplied) We report the application of genome-wide RNA-sequencing analysis for SARS-CoV-2 positive patients' mucosa. We analyzed the correlation between gene expression levels and viral load (assessed with qPCR) and found a gene signature that might be relevant for diagnosis and treatment of SARS-CoV-2 infection. We performed such analyses in samples with assigned lineage B.1 or B.1.617 (Delta). We compared the expression of these genes in negative patients and observed low abundance, thus confirming their significance.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
342 Samples
Download data: TXT
Series
Accession:
GSE184610
ID:
200184610
18.

IL-9 exacerbates SARS-CoV2 infection and associated airway inflammation

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus diseases 2019 (COVID-19) and broncho-alveolar inflammation (Merad and Martin, 2020). IL-9 induces airway inflammation and bronchial hyper responsiveness in respiratory viral illnesses and allergic inflammation (Temann et al., 1998). However, the role of IL-9 is not yet identified in SARS-CoV2 infection. Here we show that IL-9 promotes SARS-CoV2 infection and airway inflammation in K18-hACE2 transgenic (ACE2.Tg) mice, as IL-9 blockade reduces SARS-CoV2 infection and suppressed airway inflammation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
6 Samples
Download data: TSV
Series
Accession:
GSE209550
ID:
200209550
19.

TWAS-based translational genomics approach identifies IL10RB as the top candidate gene for COVID-19 host susceptibility and severity

(Submitter supplied) Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes that regulate COVID-19 host susceptibility is a critical next step. Using a translational genomics approach that integrates COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX) and perturbagen signatures, we identify IL10RB as the top key regulator of COVID-19 host susceptibility. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
48 Samples
Download data: TSV
Series
Accession:
GSE180622
ID:
200180622
20.

Elevated Myl9 reflects the Myl9-containing microthrombi in SARS-CoV-2-induced exudative vasculitis and predicts COVID-19 severity

(Submitter supplied) The mortality of coronavirus disease 2019 (COVID-19) is strongly correlated with pulmonary vascular pathology accompanied by SARS-CoV-2 infection-triggered immune dysregulation and aberrant activation of platelets. We combined histological analyses using field emission scanning electron microscopy with energy-dispersive X-ray spectroscopy analyses of the lungs from autopsy samples and single-cell RNA sequencing of peripheral blood mononuclear cells to investigate the pathogenesis of vasculitis and immunothrombosis in COVID-19. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL24676
105 Samples
Download data: CSV, MTX, TSV
Series
Accession:
GSE208337
ID:
200208337
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