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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 28, 2021 |
| Title |
1251 |
| Sample type |
SRA |
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| Source name |
Sperm
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| Organism |
Mus musculus |
| Characteristics |
cell type: Sperm
strain: C57BL/6
genotype: Mthfr -/-
generation/colony: Mat_Def_Colony
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| Treatment protocol |
Mthfr heterozygote (+/-) mice were mated in order to obtain an F1 generation of both wildtype (WT) and mutant (-/-) mice. Upon sexual maturity, these F1 generation mice were mated with +/- mice to obtain the F2 generation of WT and -/- mice. An external cohort of mice (Mat_Def_colony) was also examined, where maternal- and paternal-deficient Mthfr mice were mated to obtain Mthfr -/- male mice. Mice were sacrificed and sperm was collected from the paired caudal epididymides, washed and a 0.45% solution of NaCl and sperm pellets frozen a -80C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sperm pellets were thawed and pretreated overnight at 37°C with a lysis buffer containing EDTA, Tris, Sarkosyl, dithiothreitol (DTT) and proteinase K. The lysate was used for DNA isolation with DNeasy Blood & Tissue Kit (QIAGEN, Germany) according to the manufacturer’s protocol
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published protocols using gel-free technique (Boyle, P. Genome Biol., 2012). Briefly, ~500ng of DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing. Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplification.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.74
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT
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| Submission date |
Feb 10, 2021 |
| Last update date |
Jun 28, 2021 |
| 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 |
GPL17021 |
| Series (1) |
| GSE166586 |
Paternal MTHFR deficiency leads to reproductive decline across generations in association with hypomethylation of young retrotransposons |
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| Relations |
| BioSample |
SAMN17861207 |
| SRA |
SRX10070683 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5075966_1251.map.input.txt.gz |
20.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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