|
| Status |
Public on Jan 25, 2023 |
| Title |
HD5-0 |
| Sample type |
genomic |
| |
|
| Source name |
Sperm
|
| Organism |
Homo sapiens |
| Characteristics |
group: HD
time_point: 0
tissue: Sperm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen sperm was thawed on ice and genomic DNA isolation was performed using Qiagen DNeasy Blood & Tissue Kits (Qiagen, Canada) according to the manufacturer’s guide, with modifications. For sample were incubated overnight at 37oC in a buffer containing EDTA, Tris , sarkosyl , dithiothreitol (DTT) and proteinase K (Invitrogen, Canada). The following day, Buffer AL was added to the buffer, and incubated at 70oC for 10min and the manufacturer’s guide was continued.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Briefly, ~500ng of DNA was bisulfite converted using an EZ DNA methylation Kit, followed by whole genome amplification, enzymatic fragmentation and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged on the Illumina iScan BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
Preprocessing of the raw data files (IDAT), quality control (QC) assessment and normalization was performed using the R package minfi (version 1.36.0). The function preprocessFunnorm was used for the functional normalization of the data using internal control probes on the array to infer between-array technical vairaion. This function applies preprocessNoob function first, for background substraction and dye-bias normalization. The annotation of the array to determine the genomic location of probes was determined with IlluminaHumanMethylation450kanno.ilmn12.hg19 (version 0.6.0)
|
| |
|
| Submission date |
Aug 12, 2022 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Jacquetta Trasler |
| Organization name |
McGill University
|
| Department |
Pharmacology & Therapeutics; Human Genetics
|
| Lab |
RI-MUHC; CHHD Program
|
| Street address |
1001 Decarie Boul, Block E, ES1.4380
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4A 3J1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE211120 |
Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer [methylation array] |
| GSE211122 |
Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer. |
|
