|
| Status |
Public on Oct 14, 2024 |
| Title |
204776820083_R02C01 |
| Sample type |
genomic |
| |
|
| Source name |
normal sperm sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: sperm
cohort: SEEDS
bmi: 29.41
race: 1
creatinine: NA
specific gravity: 1.024
batch: 3
mehp: 1.9
mecpp: 8.9
mcmhp: NA
mehhp: 6.8
meohp: 4.2
mcpp: 1.9
mop: NA
mchp: NA
mbzp: 2
minp: NA
mmp: NA
mep: 6.4
mbp: 19.4
mibp: 5.5
mcnp: 1.3
mcop: 7.2
mhbp: 1.3
mhibp: 1.6
mhinch: 1.1
mcoch: 0.5
|
| Treatment protocol |
Sperm from semen was extracted using gradient method and purified DNA was isolated our previously developed method of beads, RLT and TCEPS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Illumina Protocol
|
| Label |
Cy3,Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC BeadChip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
sperm DNA methylation
Processed_methylation_data_matrix_SEEDS.RData
|
| Data processing |
Sperm DNA methylation was assessed using Illumina's EPIC Infinium Methylation Beadchip. Raw idat files were imported into R and within-array normalization and dye-bias equalization of Type I and Type II probes was performed using normal-exponential convolution method (Noob) via minfi package. Batch effects were corrected with the ComBat function in the sva package while cross-hybridizing probes were removed using the DMRcate package. probes with detection pvalue >0.01 were also exluced prior to downstream analysis.
Processed matrix contains the NOOB-normalized beta values representing the percent CpG methylation for all the CpGs that passed the preprocessing method.
|
| |
|
| Submission date |
May 15, 2024 |
| Last update date |
Oct 14, 2024 |
| Contact name |
J.Richard Pilsner |
| E-mail(s) |
[email protected]
|
| Organization name |
Wayne State University
|
| Department |
Department of Obstetrics and Gynecology
|
| Lab |
Pilsner Lab
|
| Street address |
275 E Hancock St
|
| City |
Detroit |
| State/province |
MI |
| ZIP/Postal code |
48201 |
| Country |
USA |
| |
|
| Platform ID |
GPL29753 |
| Series (1) |
| GSE267620 |
Urinary concentrations of phthalate and phthalate alternative metabolites and sperm DNA methylation: A multi-cohort and meta-analysis of men in preconception studies |
|
