Methods & materials

Preliminary research

The current state of asthma research was explored by searching the OU Library, the NCBI (National Center for Biotechnology Information, NLM/NIH) journal database and Google, with query strings including “asthma genetics latest research”, “(gene therapy) AND asthma”, “asthma pharmacogenetics”, “asthma epigenetics”, “asthma pathophysiology and pathogenesis”.

Data sourcing

To find genetic expression datasets, Gene Expression Atlas (GXA) was searched for “asthma AND Homo sapiens”, returning a list of genes' expressions extracted from research datasets. The paper ‘Phenotypic Responses of Differentiated Asthmatic Human Airway Epithelial Cultures to Rhinovirus’ (Bai, J. et al, 2015) was chosen because it’s peer-reviewed, has strong differential expression & significance values, and has the simplest experimental design. The research was funded by biotechnology companies Merck and MatTek and partly by a grant from NHLBI (1R43HL088807-01). They had no influence, only providing salaries to the research team, consisting of members from both.

Original experiment conditions

In the original experiment, 6 asthmatic and 6 non-asthmatic air-liquid interface (ALI) HAEC cultures were prepared from 12 donors and split into 24 cultures. Six of each were treated with HRV16, and the others with vehicle treatment as control. Genome-wide expression changes at 24 hours after HRV16 infection were analyzed using RNA-seq, and raw gene expression data were generated by qPCR (quantitative PCR) evaluation. Fold-change comparison data were produced by comparing complex models of each analyte.

In my research project, these sets are labelled as such:

α. asthmatic tissue with HRV16,

β. asthmatic tissue with vehicle,

γ. non-asthmatic tissue with HRV16,

δ. non-asthmatic tissue with vehicle.

See Appendix 1 for table of supplementary data files.