GEO DataSets

(Submitter supplied) The outcome of viral infection is extremely heterogeneous at the cellular level, and infected cells only sometimes activate innate immunity. Here we assess how the genetic variation inherent in viral populations contributes to this heterogeneity. We do this by developing a new approach to determine both the cellular transcriptome and full-length sequences of all viral genes in single influenza-infected cells. more...

Organism:

Canis lupus familiaris; Influenza A virus (A/WSN/1933(H1N1)); Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platforms:

GPL25643 GPL25644

2 Samples

Download data: FASTA, MTX, TSV

(Submitter supplied) Influenza A virus exhibits high rates of replicative failure due to a variety of genetic defects. As such, most viral particles cannot complete the life cycle. However, despite this failure, this virus is incredibly successful in the suppression of innate immune detection and the production of interferons, succeeding at remaining undetected in >99% of cells in tissue-culture models of infection. As the same variation that leads to replication failure can, by chance, inactivate the major innate immune antagonist in influenza A virus, NS1, what features prevent these events from triggering massive amounts of interferon production? By studying how genetic and phenotypic variation in a viral population lacking NS1 correlates with interferon production, we have built a model of the "worst-case" failure from an improved understanding of the steps at which NS1 acts in the viral lifecycle to prevent triggering of an innate immune response. more...

Organism:

Homo sapiens; Canis lupus familiaris; Influenza A virus (A/WSN/1933(H1N1))

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL32752 GPL25643

14 Samples

Download data: MTX, TSV

(Submitter supplied) Viral infection outcomes are governed by the complex and dynamic interplay between the infecting virus population and the host response. It is increasingly clear that both viral and host cell populations are highly heterogeneous, but little is known about how this heterogeneity influences infection dynamics or viral pathogenicity. To dissect the interactions between influenza A virus (IAV) and host cell heterogeneity, we examined the combined host and viral transcriptomes of thousands of individual cells, each infected with a single IAV virion. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data

(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) Host-influenza virus interplay at the transcript level has been extensively characterized in epithelial cells. Yet, there are no studies that simultaneously characterize human host and influenza A virus (IAV) genomes. We infected human bronchial epithelial BEAS-2B cells with two seasonal IAV/H3N2 strains, Brisbane/10/07 and Perth/16/09 (reference strains for past vaccine seasons) and the well-characterized laboratory strain Udorn/307/72. more...

Organism:

Homo sapiens; Influenza A virus (A/Udorn/307/1972(H3N2)); Influenza A virus (A/Brisbane/10/2007(H3N2)); Influenza A virus (A/Perth/16/2009(H3N2))

Type:

Expression profiling by high throughput sequencing

4 related Platforms

36 Samples

Download data: FA, XLSX

(Submitter supplied) The goals of this study are to compare NGS-derived whole transcriptome profiles (RNA-seq) of H5N1 infected A549 cells overexpressing either negative control mimic or miR-324-5p mimic

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: TXT

(Submitter supplied) Viral infection can dramatically alter a cell's transcriptome. However, these changes have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA sequencing to examine the transcriptional consequences of influenza virus infection. We find extremely wide cell-to-cell variation in production of viral gene transcripts -- viral transcripts compose less than a percent of total mRNA in many infected cells, but a few cells derive over half their mRNA from virus. more...

Organism:

Influenza A virus (A/WSN/1933(H1N1)); Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24389

5 Samples

Download data: FASTA, GTF, H5, TXT

(Submitter supplied) A GFP-expressing recombinant A/Puerto Rico/8/1934 influenza virus was used to infect C57BL/6 wild type mice and on day 3 post infection, lung alveolar epithelial cells (AEC) were isolated and sorted based on GFP expression. GFP+ AEC represent the infected AEC and GFP- AEC represent the bystander AEC. AEC were also sorted from uninfected mice to serve as controls.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: TXT