|
| Status |
Public on Apr 08, 2014 |
| Title |
D30-4 |
| Sample type |
genomic |
| |
|
| Source name |
peripheral mononuclear blood cells genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: F
height (cm): 153.7
age: 28.5
ethnicity: Caucasian
cell type: peripheral mononuclear blood cells
mass (kg): 59.4
bmi: 25.1
fev1 % predicted: 97
atopy: no
asthma diagnosis: yes
methacholine responsive: yes
gstp1 genotype: G allele
sample treatment: DEP
time (hr): 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from peripheral blood mononuclear cells using the Isohelix DNA isolation kit following manufacturer's instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
BeadChips were imaged using HiScan with standard recommended Illumina scanner setting
|
| Data processing |
Raw intensities extracted using GenomeStudio v2010.1. Background normalization was conducted by subtracting averaged negative probe intensity from signal A and B. Then quantile normalization was done to control for chip to chip variation. Finally, average beta is recalculated from normalized intensities: methylated intensity / (methylated + unmethylated intensities+100). Probes with bad detection p-values were removed. Also removed were probes residing on X and Y chromosomes, probes cross-hybridizing with X, Y, and autosomal chromosome sites, and probes residing at SNP sites. Array normalization was performed in R using the built-in colour-correction and background subtraction, and quantile normalization functions of the lumi package with default settings followed by peak-based correction.
|
| |
|
| Submission date |
Apr 07, 2014 |
| Last update date |
Apr 08, 2014 |
| Contact name |
Michael S. Kobor |
| Organization name |
Centre for Molecular Medicine and Therapeutics / University of British Columbia
|
| Department |
Medical Genetics
|
| Lab |
Kobor
|
| Street address |
950 West 28th Avenue
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 4H4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE56553 |
Short-term exposure to diesel exhaust is associated with dynamic changes in DNA methylation of circulating mononuclear cells in asthmatics |
|
