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Series GSE61517 Query DataSets for GSE61517
Status Public on May 25, 2018
Title Strand-specific Dual RNA-seq of Bronchial Epithelial cells Infected with Influenza A/H3N2 Viruses Reveals Splicing of Gene Segment 6 and Novel Host-Virus Interactions
Organisms 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))
Experiment type Expression profiling by high throughput sequencing
Summary 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. Strand-specific RNA-seq of the infected BEAS-2B cells allowed for simultaneous analysis of host and viral transcriptomes, in addition to pathogen genomes, to reveal changes in mRNA expression and alternative splicing (AS). In general, patterns of global and immune gene expression induced by the three IAVs were mostly shared. However, AS of host transcripts and small nuclear RNAs differed between the seasonal and laboratory strains. Analysis of viral transcriptomes showed deletions of the polymerase components (defective interfering (DI)-like RNAs) within the genome. Surprisingly, we found that the neuraminidase gene undergoes AS, and that the splicing event differs between seasonal and laboratory strains. Our findings reveal novel elements of the host-virus interaction and highlight the importance of RNA-seq in identifying molecular changes at the genome level that may contribute to shaping RNA-based innate immunity.
Overall design Examination of RNA from three different H3N2 viruses (and mock infection) at three timepoints with 3 biological replicates each.
Contributor(s) Fabozzi G, Oler AJ, Zhu J, Subbarao K, Rabin RL
Citation(s) 29976658
Submission date Sep 17, 2014
Last update date May 15, 2019
Contact name Andrew J Oler
Organization name NIAID/NIH
Department Bioinformatics and Computational Biosciences Branch (BCBB)
Lab Computational Biology Section
Street address 31 Center Drive, Room 3B62E
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (4)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL19205 Illumina HiSeq 2000 (Influenza A virus (A/Brisbane/10/2007(H3N2)))
GPL19206 Illumina HiSeq 2000 (Influenza A virus (A/Perth/16/2009(H3N2)))
Samples (36)
GSM1507295 No_virus_1h_rep1
GSM1507296 No_virus_1h_rep2
GSM1507297 No_virus_1h_rep3
BioProject PRJNA261345
SRA SRP047252

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

Supplementary file Size Download File type/resource
GSE61517_Brisbane_consensus_segments.fa.gz 4.1 Kb (ftp)(http) FA 3.2 Gb (ftp)(http) TAR
GSE61517_Perth_consensus_segments.fa.gz 4.2 Kb (ftp)(http) FA
GSE61517_Udorn_consensus_segments.fa.gz 4.1 Kb (ftp)(http) FA
GSE61517_geneStats_USeq_MISO.xlsx 22.3 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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