|
Status |
Public on Apr 08, 2014 |
Title |
D79-1 |
Sample type |
genomic |
|
|
Source name |
peripheral mononuclear blood cells genomic DNA
|
Organism |
Homo sapiens |
Characteristics |
Sex: M height (cm): 185.5 age: 25.6 ethnicity: Caucasian cell type: peripheral mononuclear blood cells mass (kg): 98.8 bmi: 28.7 fev1 % predicted: 96 atopy: yes asthma diagnosis: yes methacholine responsive: yes gstp1 genotype: G allele sample treatment: FAP 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 |
|