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SRP214490
Pseudomonas aeruginosa
167 Downloadable Samples
Illumina NovaSeq 6000, Illumina HiSeq 2500
Description
Purpose : The goal of this study was to use RNA-seq to compare transcriptional profiles under biofilm conditions with planktonic growth and explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as biofilm structure or virulence. Methods : mRNA profiles were generated for Pseudomonas aeruginosa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device or paired end mode on an Illumina Novaseq 6000. mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using bowtie2 with default settings. Overall design: mRNA profiles from Pseudomonas aeruginosa derived from static biofilm cultures grown for 12h to 48h in 96-well microtiter plates or planktonic LB cultures grown to an OD600 = 2 and deep sequenced using Illumina HiSeq 2500/NovaSeq 6000.
Publication Title
Parallel evolutionary paths to produce more than one <i>Pseudomonas aeruginosa</i> biofilm phenotype.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 47 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Vaccine research today is focused on using safer, highly purified or recombinant antigens with poor immunogenicity, which has created a need for potent adjuvants. Rational design of effective and safe mucosal adjuvants for human use necessitates a thorough understanding of the mode of action of successful candidate adjuvants.
Publication Title
Unraveling molecular signatures of immunostimulatory adjuvants in the female genital tract through systems biology.
Sample Metadata Fields
Sex, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- NextSeq 500
Description
Background: Although several studies link high levels of IL-6 and soluble IL-6 receptor (sIL-6R) with asthma severity and decreased lung function, the role of IL-6 trans-signaling (IL-6TS) in asthma is unclear. Objective: To explore the association between epithelial IL-6TS pathway activation and molecular and clinical phenotypes in asthma. Methods: Primary human bronchial epithelial cell (HBEC) air-liquid interface (ALI) cultures were stimulated with IL-6 and sIL-6R to establish an IL-6TS gene signature. Two separate RNA sequencing (RNA-seq) studies were performed: The “IL-6 vs T2 study” compared gene expression after stimulation with control medium, IL-6, IL-6/sIL-6R and IL-4/IL-13, while the “JAK1-inhibition study” addressed the effect of JAK1 inhibition on IL-6TS induced gene expression. The IL-6TS gene signature was used to stratify lung epithelial transcriptomic data obtained from asthmatics (n=103) in the U-BIOPRED cohorts by hierarchical clustering. Molecular phenotyping was based on the transcriptional profiling of epithelial brushings, pathway analysis and immunohistochemistry analysis of bronchial biopsies. Results: Activation of IL-6TS in HBEC ALI cultures reduced epithelial barrier function and induced a specific epithelial gene signature enriched in airway remodeling genes. The IL-6TS signature identified a subset (n=17) of IL-6TS High asthma patients with increased epithelial expression of IL-6TS inducible genes in absence of increased systemic levels of IL-6 and sIL-6R. The IL-6TS High subset had an increased exacerbation frequency (p=0.028), blood (>300/µl; p=0.0028) and sputum (>20%; p=0.007) eosinophilia, and submucosal infiltration of CD4 T cells, CD8 T cells (p<0.001) and macrophages (p=0.001). In bronchial brushings, TLR pathway genes were up-regulated while the expression of epithelial tight junction genes was reduced (all with q<0.05). Sputum sIL-6R levels correlated with sputum markers of remodeling and innate immune activation, in particular YKL-40, MMP3, IL-8 and IL-1ß (all with q<0.001). Conclusions: Local lung epithelial IL-6TS activation in absence of type 2 airway inflammation defines a novel subset of asthmatics and may drive airway inflammation and epithelial dysfunction in these patients. Overall design: Primary human bronchial epithelial cells grown and differentiated on air-liquid interface were stimulated basolaterally for 24h with cytokines corresponding to IL-6TS (IL-6 + sIL-6R), IL-6 alone, a Type 2 immune response (IL-4 + IL-13) or media alone as non-stimulated control. Each stimulation condition was done in triplicates. Cells were lysed, the RNA isolated and converted into libraries then used for next generation sequencing in order to identify genes that were up- or downregulated in response to the different stimulations.
Publication Title
Epithelial IL-6 trans-signaling defines a new asthma phenotype with increased airway inflammation.
Sample Metadata Fields
Specimen part, Subject
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