|
| Status |
Public on May 03, 2020 |
| Title |
203259060137/203259060137_R06C01 |
| Sample type |
genomic |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
participant id: discovery_27
Sex: male
age: 46
tissue: Blood
bmi: 24.46029542
bmi group: lean
cohort: discovery
sentrix_id: 203259060137
sentrix_position: R06C01
|
| Treatment protocol |
Semen samples were processed within one hour of sample production and analysed for sperm concentration, motility and average progressive velocity. All semen samples were within normal parameters according to World Health Organization criteria. Samples underwent gradient centrifugation to select for motile spermatozoa. The processed samples were microscopically assessed for cell purity.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from 200 µL buffy coat derived from whole blood was extracted using Qiagen QIAamp DNA Blood Mini Kit. DNA from the pellet of motile spermatozoa was extracted phenol-chloroform extraction. DNA extracted from whole blood and sperm was quality controlled using a Qubit 3.0 Fluorometer. DNA was stored in -80°C prior to bisulphite conversion.
|
| Label |
Cy3, Cy5
|
| Label protocol |
DNA was sodium bisulphite-treated using the Zymo EZ 96 DNA methylation kit.
|
| |
|
| Hybridization protocol |
DNA methylation was measured using the Illumina Infinium MethylationEPIC BeadChip according to the manufacturer's protocol.
|
| Scan protocol |
DNA methylation quantification was run on an Illumina iScan System according to the manufacturer's protocol. The Illumina Genome Studio software was used to extract the raw signal intensities of each probe.
|
| Description |
discovery_blood_27
whole blood sample
|
| Data processing |
DNA methylation data was processed using the wateRmelon package in R. An outlier analysis was performed using the outlyx() function. The 59 non-CpG SNP probes on the array were used to confirm matched samples. 9,779 probes were removed from the discovery data because more than 5% samples displayed a detection P value > 0.05. 3,337 probes were removed because of having a bead count < 3. Probes containing SNPs in close proximity to the CpG site as well as cross-reactive probes were filtered using annotated lists. The final discovery data set comprised 704,356 CpG sites. Data was normalized using the dasen() function. The lean and obese replication cohorts were processed together experimentally and therefore jointly pre-processed and normalized using the same parameters as for the discovery dataset. A total of 697,442 probes survived quality control and filtering in the replication data. DNA methylation was analysed and reported as beta values.
|
| |
|
| Submission date |
Apr 24, 2020 |
| Last update date |
May 03, 2020 |
| Contact name |
Sarah Marzi |
| E-mail(s) |
s.marzi@imperial.ac.uk
|
| Organization name |
Imperial College London
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE149318 |
DNA methylation covariation in human whole blood and sperm |
|
