GEO DataSets

(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 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) 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:

Severe acute respiratory syndrome coronavirus 2; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29320 GPL24676

10 Samples

Download data: CSV

(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

(Submitter supplied) The ongoing pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates strategies to identify prophylactic and therapeutic drug candidates for rapid clinical deployment. Here we describe a screening pipeline for the discovery of efficacious SARS-CoV-2 inhibitors. Two high-throughput, high-content imaging infection assays (one using HeLa cells expressing SARS-CoV-2 receptor ACE2 and the other using lung epithelial Calu-3 cells) were developed and used to screen ReFRAME, a best-in-class drug repurposing library. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28997

10 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 has caused a historic pandemic of respiratory disease (COVID-19) and current evidence suggests severe disease is associated with dysregulated immunity within the respiratory tract1,2. However, the innate immune mechanisms that mediate protection during COVID-19 are not well defined. Here we characterize a mouse model of SARS-CoV-2 infection and find that early CCR2-dependent infiltration of monocytes restricts viral burden in the lung. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: MTX, TSV

(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) 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) We sought to define the host immune response, a.k.a, the “cytokine storm” that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 publicly available transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a ‘seed’ gene; ACE2 was rationalized because the receptor it encodes enables the virus that causes Covid-19, SARS-CoV-2, to enter host cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TXT

(Submitter supplied) We sought to define the host immune response, a.k.a, the “cytokine storm” that has been implicated in fatal COVID-19 using an AI-based approach. Over 45,000 publicly available transcriptomic datasets of viral pandemics were analyzed to extract a 166-gene signature using ACE2 as a ‘seed’ gene; ACE2 was rationalized because the receptor it encodes enables the virus that causes Covid-19, SARS-CoV-2, to enter host cells. more...

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28997

8 Samples

Download data: TXT

(Submitter supplied) Purpose of experiment was to perform transcriptomic analysis on C57Bl/6 mice infected with different doses of SARS CoV MA15 at 4 different days post infection.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

92 Samples

Download data: TXT

(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) Here we report the transcriptional response to SARS-CoV-2 in Syrian golden hamsters and compare it to the host response against Influenza A virus. The virus replicates fast to high titers in the respiratory tract followed by a local and systemic inflammatory response. A roust IFN-I reponse is mounted and lasts at leaset fourteen days in distal tissues together with other lasting transcriptional changes.

Organism:

Mesocricetus auratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24490

215 Samples

Download data: CSV

(Submitter supplied) COVID-19, caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple-organ failure, but little is known about its pathophysiology. Here, we generated single-cell atlases of 23 lung, 16 kidney, 15 liver and 18 heart COVID-19 autopsy donor tissue samples, and spatial atlases of 14 lung donors. Integrated computational analysis uncovered substantial remodeling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of myofibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24268 GPL27644

188 Samples

Download data: CSV, H5, TXT

(Submitter supplied) The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

80 Samples

Download data: DCC, TSV, TXT

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

Organism:

Homo sapiens; blank sample

Type:

Expression profiling by high throughput sequencing; Other

5 related Platforms

1194 Samples

Download data: DCC

(Submitter supplied) The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL29514

330 Samples

Download data: PKC, XLSX

(Submitter supplied) The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. more...

Organism:

Homo sapiens; blank sample

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

784 Samples

Download data: DCC, PKC, XLSX

(Submitter supplied) We present evidence on how a lung epithelial cell culture system based on human induced pluripotent stem cells (hiPSC) could emerge as a relevant and sensitive platform for modelling SARS-CoV-2 infection. In order to develop a human model system, we differentiated hiPSC into lung epithelial lineage (airway and alveolar cells) through a three-step protocol. De novo generated cells were authenticated by spatiotemporal expression of stage specific markers including SOX2, FOXJ1 and CC10 in proximal cells and SOX9, FOXP2, SFTPC, MUC5AC, and CC10 in distal cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TXT