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Series GSE106379 Query DataSets for GSE106379
Status Public on Oct 24, 2018
Title Genetics, sex and life experience influence DNA methylation in the mouse
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Methylation of DNA is an essential epigenetic mark in mammals, intimately involved in gene regulation. The extent to which genetics, sex, and life experience influence genomic DNA methylation patterns are matters of intense current interest. We addressed this issue by intercrossing inbred mouse strains and analyzing DNA methylation at the base-pair level across the genome in somatic tissue from parents and from age-matched offspring of multiple families. In comparison across genotype, tens of thousands of differentially methylated CpG residues and thousands of differentially methylated regions were detected. Differential methylation at these loci was preserved on parental alleles in offspring, suggesting that CpG methylation is a very stable epigenetic mark largely preserved across generation, correlating with DNA sequence. In comparison of autosomal DNA methylation patterns across sex, thousands of differentially methylated CpG residues and hundreds of differentially methylated regions were detected, consistent with known biological parameters that differ between males and females. Finally, comparison of individual groups of animals within our study revealed a CpG methylation pattern that likely results from pregnancy and/or lactation that was restricted to female animals who had borne offspring, signifying that CpG methylation may provide a record of major life events. Collectively, our results demonstrate the stability of CpG methylation across generation, clarify the interplay of epigenetics with genetics and sex, and suggest that CpG methylation may serve as an epigenetic record of life events.
Overall design Methylation profiles of C57BL/6N mice, C3H/HeN mice, and their offspring were determined by whole-genome bisulfite sequencing.
Contributor(s) Wade PA, Grimm SA, Takaku M
Citation(s) 30659182, 29973619, 37020391
Submission date Oct 31, 2017
Last update date May 12, 2023
Contact name Paul A Wade
Phone 919-541-3392
Organization name NIEHS
Department Laboratory of Molecular Carcinogenesis
Street address 111 TW Alexander Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (36)
GSM2836889 B6_M_1
GSM2836890 B6_M_2
GSM2836891 B6_M_3
BioProject PRJNA416505
SRA SRP123210

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE106379_B6.FOXA1_ChIP.downsampled.bigWig 312.7 Mb (ftp)(http) BIGWIG
GSE106379_B6.input.downsampled.bigWig 310.2 Mb (ftp)(http) BIGWIG
GSE106379_C3.FOXA1_ChIP.downsampled.bigWig 311.1 Mb (ftp)(http) BIGWIG
GSE106379_C3.input.downsampled.bigWig 309.7 Mb (ftp)(http) BIGWIG
GSE106379_CpG.meth_cts_per_site.txt.gz 464.4 Mb (ftp)(http) TXT
GSE106379_CpG.unmeth_cts_per_site.txt.gz 370.0 Mb (ftp)(http) TXT
GSE106379_RAW.tar 2.3 Gb (http)(custom) TAR (of BIGWIG)
GSE106379_local_genome_SNVs.txt.gz 11.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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