NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE118773 Query DataSets for GSE118773
Status Public on Dec 10, 2019
Title Cell-to-cell variation in defective virus expression and effect on host response during influenza virus infection
Organisms Homo sapiens; Canis lupus familiaris; Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Experiment type Expression profiling by high throughput sequencing
Other
Summary 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. We observed substantial variability of viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show a correlation between DVGs and viral-induced variation of the host transcriptional program and an association between differential induction of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single cell level improve our understanding of the complex virus-host interplay during influenza infection.
 
Overall design Dataset consists of 12 single-cell RNA-seq datasets generated from 10X Genomics Chromium 3' platform with v2 chemistry, 20 conventional bulk RNA-seq datasets generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module, and one viral genome sequencing dataset generated from multi-segment reverse-transcription PCR (M-RT-PCR) products followed by library preparation with Nextera DNA library prep kit.
 
Contributor(s) Wang C, Forst CV, Chou T, Geber A, Wang M, Hamou W, Smith M, Sebra R, Zhang B, Zhou B, Ghedin E
Citation(s) 31937643
Submission date Aug 20, 2018
Last update date Feb 03, 2020
Contact name Chang Wang
E-mail(s) chang.wang@nyu.edu
Organization name New York University
Department Biology
Lab Ghedin
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platforms (7)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL25466 Illumina HiSeq 2500 (Homo sapiens; Influenza A virus (A/Puerto Rico/8/1934(H1N1)))
Samples (33)
GSM3347396 single-cell RNA-seq dataset: mock-infected A549 cells
GSM3347397 single-cell RNA-seq dataset: PR8-infected A549 cells at 6hpi
GSM3347398 single-cell RNA-seq dataset: PR8-infected A549 cells at 12hpi
Relations
BioProject PRJNA486793
SRA SRP158405

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE118773_RAW.tar 97.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap