|
| Status |
Public on Jul 28, 2014 |
| Title |
Healthy01-HRV |
| Sample type |
genomic |
| |
|
| Source name |
Nasal Epithelial cell
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Non-Asthmatic
culture condition: Infected
gender: Female
ethnicity: White/caucasian
atopy: No
asthma medication: No
|
| Treatment protocol |
When NEC cultures reached 80-90% confluence, cells were infected either with HRV-16 (multiplicity of infection=2) or phosphate buffered saline (PBS, Mock) in a final volume of 100µL Bronchial Epithelial Basal Medium (Lonza) for 1hr at 33°C with mild shaking. Infection media was then removed and cells washed twice with warm PBS then 500µL of fresh BEGM was added and cultures returned to 37°C for 48hrs.
|
| Growth protocol |
Nasal epithelial cells (NECs) were plated in 12-well dishes pre-coated with 0.2 mg/mL Type I purified collagen (Vitrogen 100, Advanced Biomatrix Corp.) in complete Bronchial Epithelial Cell Media (BEGM, Lonza) and incubated at 37°C with 5% CO2 until 80-90% confluence was achieved. Cells were then trypsinized (0.25% Trypsin EDTA), harvested, split and sub cultured onto collagen coated 24-well plates and maintained in BEGM (passage 1).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total nucleic acids were isolated from nasal cell cultures using TRI reagent (Life Technologies), phenol/chloroform extraction and ethanol precipitation.
|
| Label |
Cy3, Cy5
|
| Label protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol
|
| |
|
| Hybridization protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Scan protocol |
BeadStudio software v3.2
|
| Description |
Healthy infected
H01-HRV
|
| Data processing |
For microarray analysis, log2 ratios of the methylated and unmethylated probes (i.e. M values) were quantile normalized and then subject to linear modeling using Empirical Bayes variance correction. Tests of contrast on linear model parameters were used to evaluate pairwise comparisons of interest (Asthma x Healthy pre-HRV, A x H post-HRV, HRV changes in A, HRV changes in H, A x H HRV changes). Statistical analyses of microarray data were performed in R (v2.15.2) using packages from the Bioconductor.
|
| |
|
| Submission date |
Nov 04, 2013 |
| Last update date |
Jul 28, 2014 |
| Contact name |
Peter McErlean |
| Organization name |
Northwestern University
|
| Department |
Allergy Immunology
|
| Lab |
Avila
|
| Street address |
240 E. Huron, McGaw M-530h
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60613 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE52074 |
Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects |
|
