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Series GSE63900 Query DataSets for GSE63900
Status Public on Nov 02, 2015
Title Dual RNA-sequencing of nontypeable Haemophilus influenzae and host cell transcriptomes reveals new aspects of host-pathogen interface
Organisms Haemophilus influenzae; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Characterization of host-pathogen interactions is critical for the development of next-generation therapies and vaccines. Classical approaches involve the use of transformed cell lines and/or animal models which may not reflect the complexity and response of the human host. We reconstituted the ciliated human bronchial epithelium in vitro using primary bronchial epithelial cells to simultaneously monitor the infection-linked global changes in nontypeable Haemophilus influenzae (NTHi) and infected host epithelia gene expression by dual RNA-seq. Acquisition of a total of nearly 2,5 billion sequences allowed construction of high-resolution strand-specific transcriptome maps of NTHi during infection of host mucosal surface and monitoring of metabolic as well as stress-induced host-adaptation strategies of this pathogen. As a part of our screening, we identified a global profile of noncoding transcripts that are candidate small RNAs regulated during human host infection in Haemophilus species. Temporal analysis of host mRNA signatures revealed significant dysregulation of target cell cytoskeleton elicited by bacterial infection, with a profound effect on intermediate filament network of bronchial epithelium. Our data provide a robust and comprehensive catalogue of regulatory responses that drive NTHi pathogenesis and gives novel insights into complex crosstalk between the host and the invading pathogen.
Overall design Primary human bronchial epithelium was infected with NTHi at a multiplicity of 100:1. Total RNA was isolated at 1, 6, 24 and 72 h post-infection in three biologically-independent experiments and cDNA libraries were prepared and sequenced with Illumina HiSeq 2500 sequencer. At each time point, between 60 and 180 million total reads per sample were obtained of which approximately one-third could be aligned to non-rRNA regions of the bacterial and human genomes
Contributor(s) Baddal B, Muzzi A, Censini S, Calogero RA, Torricelli G, Guidotti S, Taddei AR, Covacci A, Pizza M, Rappuoli R, Soriani M, Pezzicoli A
Citation(s) 26578681
Submission date Dec 05, 2014
Last update date May 15, 2019
Contact name Raffaele A Calogero
Phone ++39 0116706454
Organization name University of Torino
Department Molecular Biotechnology Center
Lab Bioinformatics and Genomics Unit
Street address Via Nizza 52
City Torino
State/province To
ZIP/Postal code 10126
Country Italy
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL19560 Illumina HiSeq 2500 (Haemophilus influenzae)
Samples (24)
GSM1560001 t1_Hi726ctr_rep1
GSM1560002 t1_Hi726ctr_rep2
GSM1560003 t1_Hi726ctr_rep3
BioProject PRJNA270371
SRA SRP051182

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE63900_HTSEQ_raw_counts.txt.gz 915.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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