GEO DataSets

(Submitter supplied)  In this study, we elucidated defective viral genome generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from RNA-seq datasets of in vitro infections and autopsy lung tissues of COVID-19 patients.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: TXT

(Submitter supplied) Defective viral genomes of the copy-back type (cbDVGs) are generated during RSV infectin and are suggested to impact the clinical outcome. Here in this study we selected the nasal secretions from 13 hospitalized pediatric pateints, including both cnDVG+ and cbDVG-, to perform RNA-seq to understand the impact of cbDVGs on patient transcriptome.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

13 Samples

Download data: TXT

(Submitter supplied) Virus and host factors contribute to cell-to-cell variation in viral infection and determine the outcome of the overall infection. However, the extent of the variability at the single cell level and how it impacts virus-host interactions at a systems level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. more...

Organism:

Homo sapiens; Canis lupus familiaris; Influenza A virus (A/Puerto Rico/8/1934(H1N1))

Type:

Expression profiling by high throughput sequencing; Other

7 related Platforms

33 Samples

Download data: TXT

(Submitter supplied) Pathogenic mechanisms underlying severe SARS-CoV2 infection remain largely unelucidated. High-throughput sequencing technologies that capture genome and transcriptome information are key approaches to gain detailed mechanistic insights from infected cells. These techniques readily detect both pathogen and host-derived sequences, providing a means of studying host-pathogen interactions. Recent studies have reported the presence of host-virus chimeric (HVC) RNA in RNA-seq data from SARS-CoV2 infected cells and interpreted these findings as evidence of viral integration in the human genome as a pathogenic mechanism. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TXT

(Submitter supplied) Replication defective viral genomes (DVGs) generated during virus replication are the primary triggers of antiviral immunity in many infections. However, DVGs also provide viruses with an evolutionary advantage by facilitating virus persistence. Why and how DVGs and the host interact to achieve these two divergent functions remains unknown. We report that DVGs engage a MAVS-mediated antiviral response that promotes apoptosis on highly infected cells while protecting cells dominated by DVGs from death. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) Single Cell Sequencing of SARS-CoV2 Infected Human Nasal Epithelial Cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: MTX, TSV, XLSX

(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

(Submitter supplied) We have collected nasal cell swab samples from SARS-CoV-2 infected confirmed COVID-19 patients. Both virus and host RNA were extracted and sequenced by RNA-seq. We mapped and assembled virus sequences and in this study transcriptional profile of host due to virus infection.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TXT

(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) Type 1 interferons (IFN-I) exert pleiotropic biological effects during viral infections, balancing virus control and immune-mediated pathology and have been successfully employed for the treatment of viral diseases. In humans, there are twelve IFN-alpha (α) subtypes, which activate downstream signalling cascades and result in a distinct pattern of immune responses and differential antiviral responses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

60 Samples

Download data: XLSX

(Submitter supplied) SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minue reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. more...

Organism:

Severe acute respiratory syndrome coronavirus 2

Type:

Other

Platform:

GPL28588

4 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. more...

Organism:

Escherichia coli; Severe acute respiratory syndrome coronavirus 2; Chlorocebus sabaeus

Type:

Other

Platforms:

GPL21222 GPL28836 GPL28588

17 Samples

Download data: WIG

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676

493 Samples

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(Submitter supplied) We examined host gene expression as a function of time in SARS-CoV-2-infected individuals.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) We examined host gene expression in human airway epithelial cells following infection at 3 or 7 days post infection (DPI) with SARS-CoV-2

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TXT

(Submitter supplied) We examined host gene expression across infection status, viral load, age, and sex among RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong interferon-driven antiviral response and reduced transcription of ribosomal proteins. Expression of interferon-responsive genes, including ACE2, increased as a function of viral load. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

484 Samples

Download data: TXT

(Submitter supplied) SARS-CoV-2 coronavirus is one of the largest RNA viruses (26-32kb) and has emerged as a major threat to global public health. The resulting pandemic has caused global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype and a 382 deletion SARS-CoV-2 virus inside cells. We identified twelve potentially functional structural elements along the SARS-CoV-2 genome and observed that subgenomic viral RNA (sgRNAs) contains different structures that could be important for their functions using direct RNA sequencing. more...

Organism:

Chlorocebus

Type:

Other

4 related Platforms

14 Samples

Download data: CSV, TSV