|
| Status |
Public on May 19, 2020 |
| Title |
201516330013_R07C01 |
| Sample type |
genomic |
| |
|
| Source name |
blood samples
|
| Organism |
Homo sapiens |
| Characteristics |
age: <= 25
Sex: M
person id: 72684
disease state: normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
bisulphite conversion of 500 ng of each DNA sample was performed using the EZ DNA Methylation-Lightning Kit according to the manufacturer’s protocol (Zymo Research, Orange, CA).
|
| Label |
biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP)
|
| Label protocol |
Illumina Infinium HD Methylation protocol
|
| |
|
| Hybridization protocol |
Then, bisulfite-converted DNA was used for hybridization on the Infinium HumanMethylation EPIC BeadChip, following the Illumina Infinium HD Methylation protocol. Briefly, a whole genome amplification step was followed by enzymatic end-point fragmentation and hybridization to HumanMethylation EPIC BeadChips at 48°C for 17 h, followed by single nucleotide extension. The incorporated nucleotides were labelled with biotin (ddCTP and ddGTP) and 2,4-dinitrophenol (DNP) (ddATP and ddTTP).
|
| Scan protocol |
the BeadChip was scanned using the Illumina HiScan SQ scanner. The intensities of the images were extracted using in-house software written for the R statistical computing environment. The methylation score for each CpG was represented as a β-value according to the fluorescent intensity ratio representing any value between 0 (unmethylated) and 1 (completely methylated).
|
| Description |
normal blood sample
|
| Data processing |
DNA methylation (DNAm) data were pre-processed and normalized using in-house software written for the R statistical computing environment, including background and color bias correction, quantile normalization, and Beta MIxture Quantile dilation (BMIQ) procedure to remove type I/type II probes bias, as described elsewhere (Fiorito et al., 2017). DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values). Cross-reactive and polymorphic probes - with minor allele frequency greater than 0.01 in Europeans (Y. A. Chen et al., 2013) - were excluded. Methylation measures were set to missing if the detection p-value was greater than 0.01. Samples with the bisulfite conversion control fluorescence intensity lower than 10,000 for both type I and type II probes and those with total call rate lower than 95% were excluded. Finally, samples were excluded if the predicted sex (based on chromosome X methylation) did not match that self-reported.
DNAm levels were expressed as the ratio of the intensities of methylated cytosines over the total intensities (β values).
|
| |
|
| Submission date |
Mar 30, 2020 |
| Last update date |
May 19, 2020 |
| Contact name |
Oliver Robinson |
| E-mail(s) |
o.robinson@imperial.ac.uk
|
| Phone |
02075942067
|
| Organization name |
IMPERIAL COLLEGE LONDON
|
| Department |
School of Public Health
|
| Lab |
MRC Centre for Environment and Health
|
| Street address |
St Mary's Campus, Norfolk Place
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
W21PG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE147740 |
DNA methylation analysis of human peripheral blood mononuclear cell collected in the AIRWAVE study |
|
