GEO DataSets

(Submitter supplied) Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial 5 infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. more...

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL29320

10 Samples

Download data: CSV

(Submitter supplied) We performed transcriptomic profiling of cells derived from human pluripotent stem cells (PSCs) using our previously described distal lung directed differentiation protocol to generate alveolar type II epithelial-like cells (iAT2s). We used the SPC2 human iPSC line containing a SFTPC-tdTomato knock-in reporter. SFTPC-tdTomato+ iAT2s were sorted on day 41 and again on day 69 of differentiation. iAT2s were single-cell passaged in self-renewing 3D alveolosphere culture approximately every 2 weeks through day 194 of differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: CSV

(Submitter supplied) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), may result in acute respiratory distress syndrome (ARDS), multi-organ failure and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. Here, we describe a human 2D air-liquid interface culture system which was characterized by confocal-, electron-microscopy and single cell mRNA expression analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: TSV

(Submitter supplied) Bulk RNA sequencing was performed on control and SARS-CoV-2 infected 2D bronchioalveolar-like and small airway cultures Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), may result in acute respiratory distress syndrome (ARDS), multi-organ failure and death. The alveolar epithelium is a major target of the virus, but representative models to study virus host interactions in more detail are currently lacking. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: CSV

(Submitter supplied) The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate investigation of pathologies including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia. We generated long-term feeder-free, chemically-defined culture of distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: MTX, TSV

(Submitter supplied) Although the main cellular target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is thought to be alveolar cells, the absence of their tractable culture system has precluded the development of a clinically-relevant SARS-CoV-2 infection model. Here, we established an efficient human alveolosphere culture method and sphere-based drug testing platform for SARS-CoV-2. Alveolospheres exhibited indolent growth in a Wnt and R-spondin dependent manner. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: CSV

(Submitter supplied) We performed RNAseq analysis on primary human airway epithelial cultures either mock infected (PBS) or infected with SARS-CoV-2. Transcriptional profiling studies found that infected pHAE cells had a molecular signature dominated by pro-inflammatory cytokines and chemokine induction, including IL-6, TNFα, CXCL8, and identified NF-κB and ATF4 as key drivers of this pro-inflammatory cytokine response. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) All coronaviruses known to have recently emerged as human pathogens probably originated in bats1. Here we use a single experimental platform based on immunodeficient mice implanted with human lung tissue (hereafter, human lung-only mice (LoM)) to demonstrate the efficient in vivo replication of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as well as two endogenous SARS-like bat coronaviruses that show potential for emergence as human pathogens. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25526

13 Samples

Download data: CSV

(Submitter supplied) We conducted a high-throughput drug repositioning screen using the LOPAC®1280 and the ReFRAME drug libraries to identify existing drugs that harbor antiviral activity against SARS-CoV-2, in a Vero E6 cell-based assay. We additionally performed RNA sequencing on control and SARS-CoV-2 infected Vero E6 cells to study the biological changes after SARS-CoV-2 infection and to elucidate the potential mechanisms underlying the positive hits identified from our high-throughput screen. more...

Organism:

Chlorocebus sabaeus; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28837 GPL28836

6 Samples

Download data: TXT

(Submitter supplied) Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), a global pandemic characterized by respiratory illness and an exaggerated immune response. Age (>60 years) is a significant risk factor for developing severe COVID-19. However, the underlying mechanisms of how aging impacts SARS-CoV-2 infection and the host response are largely unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

36 Samples

Download data: TXT

(Submitter supplied) We performed unbiased transcriptomic profiling on organoids cultures after SARS-CoV-2 infection to gain insights into AT2s response to SARS-CoV-2 infection.

Organism:

Homo sapiens; Severe acute respiratory syndrome coronavirus 2

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28694 GPL20795

6 Samples

Download data: CSV

(Submitter supplied) The SARS-CoV-2 novel coronavirus global pandemic (COVID-19) has led to millions of cases and hundreds of thousands of deaths globally. While older adults appear at high risk for severe disease, hospitalizations and deaths due to SARS-CoV-2 among children have been relatively rare. Integrating single-cell RNA sequencing (scRNA-seq) of developing mouse lung with temporally-resolved immunofluorescence in mouse and human lung tissue, we found expression of SARS-CoV-2 Spike protein primer TMPRSS2 was highest in ciliated cells and type I alveolar epithelial cells (AT1), and TMPRSS2 expression increased with aging in mice and humans. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: CSV

(Submitter supplied) In an attempt to understand the mode of antiviral action of lactoferrin on SARS-CoV-2 infection, we focused on the effect of lactoferrin on uninfected cells. We decided to use a physiologically relevant cell model of iPSC derived- alveolar epithelial cells (the iAEC2). We specifically focused on antiviral pathway triggered by lactoferrin on treated cells that could explain a cell-mediated effect of lactoferrin on viral replication

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

(Submitter supplied) Detailed knowledge about dynamics of SARS-CoV-2 infection in vivo is important for unraveling the viral and host response factors that contribute to COVID-19 pathogenesis. The unknown dose and exposure timing in human infections makes the needed well-controlled time course studies impossible and thus animal models of disease are essential to fill in the gaps in our understanding of disease progression. more...

Organism:

Chlorocebus aethiops

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29061

20 Samples

Download data: TAR

(Submitter supplied) We performed single-cell RNA sequencing on human bronchial epithelial cells infected with SARS-CoV-2. Results revealed a detailed characterization of genes, cell types, and cell state changes asociated with SARS-CoV-2 infection in the human airway.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: H5AD, MTX, TSV

(Submitter supplied) Lung and hindgut directed differentiations with multiple protocols and time points

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: TXT

(Submitter supplied) The goal of our study is to establish a method to propagate human pneumocytes efficiently in a large scale. While human pneumectomy-derived lung epithelial cells (LECs) showed efficient long-term growth when co-cultured with irradiated NIH-3T3, they do not express molecular markers of mature pneumocytes or airway cells in this condition. Removal of feeders causes differentiation toward airway club cell-like phenotype, and an induction treatment with combination of small molecules and growth factors is required to differentiate them toward pneumocytes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21272

8 Samples

Download data: TXT

(Submitter supplied) To identify a causative variant and effector gene responsible for a 2-fold increased risk of severe COVID-19, a multi-omics platform was deployed. A combination of ATAC-seq, ChIP-seq, Micro Capture-C and NuTi Capture-C were used to characterize a range of cell types, including epithelial, fibroblast, endothelial, immune and erythroid cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL18573

34 Samples

Download data: BW

(Submitter supplied) To identify regulatory interactions in erythroid, fibroblast and endothelial cells Micro Caputre-C was carried outfrom the promoters of active genes as well as the rs17713054 containing enhancer.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

14 Samples

Download data: BW, TXT

(Submitter supplied) To identify regions of open chromatin ATAC-seq was carried out in Blood outgrowth endothelial cells (BOECs) and NCI-H441 Epithelial cells

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BW