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| Status |
Public on Jan 25, 2023 |
| Title |
Sperm, Testicular Cancer, 18month [TC29-3] |
| Sample type |
SRA |
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| Source name |
Sperm
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Sperm
treatment: Testicular Cancer
time: 18 months
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| 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.
Using 1ug of DNA from each sample, whole genome bisulfite sequencing (WGBS) library preparation and targeting bisulfite sequencing was libraries were performed as described previously. Briefly, DNA was sonicated to obtain 300-400bp fragments, proceeded by DNA-end repair, 3’-end adenylation, adaptor ligation and clean up, according to the KAPA High Throughput Library Preparation kit protocol (Roche/KAPA Biosystems). Samples were then bisulfite converted using the EpiTect Fast DNA bisulfite kit (Qiagen) followed by 9-12 cycles of PCR amplification. The final WGBS libraries were purified using Agencourt AMPure Beads (Beckman Coulter) and were then enriched using our human sperm specific panel, using the SeqCap Epi Enrichment System protocol developed and optimized by Roche NimbleGen. Equal amounts of the multiplexed WGBS libraries (84ng each) were combined and hybridized to the human sperm specific capture panel at 47C for 72h. The captured libraries were washed, recovered and PCR amplified before final purification was conducted. The final capture libraries were sequenced one a single lane of the Illumina HiSeq4000 system using 100-bp paired end sequencing.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
library strategy: Customized 5-methyl-cytosine capture sequencing (MCC-Seq)
Raw fastq files were trimmed of adaporter sequences with trimmoatic (version 0.36)
Trimmed reads were aligned to the hg19 genome using bismark aligner (version 0.18.1)
Duplicate aligned reads (if they have the same 5' alignment positions for bother paired in paired-end reads) are removed with picard tools (version 2.9.0). All duplicated reads are remvoed and only the best pairs, based on alignment score) is kepit
Methylation information was extracted from the bisulfite read aligment files for indivudial cytosines using bismark (version 0.18.1)
Assembly: hg19
Supplementary files format and content: CpG methylation profiles for individual samples as a txt file. Files contains the following columns: chr, start, stop, number C on forward (fw), number of total fw, methylation fw, numer of C on reverse (rv), number total rv, methylation rv, total C, total reads, total methylation
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| Submission date |
Aug 12, 2022 |
| Last update date |
Jan 25, 2023 |
| Contact name |
Jacquetta Trasler |
| Organization name |
McGill University
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| Department |
Pharmacology & Therapeutics; Human Genetics
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| Lab |
RI-MUHC; CHHD Program
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| Street address |
1001 Decarie Boul, Block E, ES1.4380
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4A 3J1 |
| Country |
Canada |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE211121 |
Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer [MCC-Seq] |
| GSE211122 |
Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer. |
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| Relations |
| BioSample |
SAMN30281569 |
| SRA |
SRX17040545 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6450984_TC29-3_original.txt.gz |
174.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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