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| Status |
Public on Apr 17, 2024 |
| Title |
Sperm, TT genotype, FASD5 |
| Sample type |
SRA |
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| Source name |
Sperm
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| Organism |
Mus musculus |
| Characteristics |
tissue: Sperm
Sex: male
strain: C57Bl/6J
genotype: TT
treatment: FASD
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| Treatment protocol |
Mthfr TT mice and wild-type mice as control (Mthfr CC) at four weeks of age were given one of 3 different diets: control (CD, 2mg folic acid/kg diet), folate-deficient (FD, 0.3mg folic acid/kg diet) and moderate dose folic acid-supplemented (FASD, 5-fold supplemented: 10 mg folic acid/kg diet) diets. They were maintained on these diets for four months. At the end of diet treatments mice were sacrificed and tissues and organs were collected. Mature spermatozoa from paired cauda epididymides were collected and kept frozen at -80oC until use.
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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 1-2ug of DNA from each sample, whole genome bisulfite sequencing (WGBS) library preparation was 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)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw fastq files were trimmed of adaporter sequences with trimmoatic (version 0.36)
Trimmed reads were aligned to the mm10 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 removed and only the best pair, based on alignment score, is kept
Methylation information was extracted from the bisulfite read aligment files for indivudial cytosines using bismark (version 0.18.1)
Assembly: mm10
Supplementary files format and content: CpG methylation profiles for individual samples as a txt file. Files contains the following columns: chrBase, chr, base, strand, coverage, freqC, freqT
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| Submission date |
Aug 11, 2023 |
| Last update date |
Apr 17, 2024 |
| 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 |
GPL24247 |
| Series (2) |
| GSE240712 |
Sperm DNA methylation defects in a new mouse model of the 5,10-methylenetetrahydrofolate reductase 677C>T variant and correction with moderate dose folic acid supplementation. |
| GSE240713 |
Impact of Folate Status on the Sperm DNA Methylome of Mice with the 677C>T Variant in 5,10-Methylenetetrahydrofolate Reductase |
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| Relations |
| BioSample |
SAMN36953942 |
| SRA |
SRX21346973 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7708209_TT_FASD_186-1.readset_sorted.dedup.map.input.txt.gz |
130.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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