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Sample GSM5075954 Query DataSets for GSM5075954
Status Public on Jun 28, 2021
Title Mut_G1_P3-4-EG
Sample type SRA
 
Source name Sperm
Organism Mus musculus
Characteristics cell type: Sperm
strain: C57BL/6
genotype: Mthfr -/-
generation/colony: F1
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.
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.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Feb 10, 2021
Last update date Jun 28, 2021
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 GPL17021
Series (1)
GSE166586 Paternal MTHFR deficiency leads to reproductive decline across generations in association with hypomethylation of young retrotransposons
Relations
BioSample SAMN17861219
SRA SRX10070671

Supplementary file Size Download File type/resource
GSM5075954_Mut_G1_P3-4-EG.map.input.txt.gz 22.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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