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Series GSE248002 Query DataSets for GSE248002
Status Public on Jan 15, 2024
Title Nonlinear DNA methylation trajectories in aging male mice [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.
 
Overall design RNA sequencing with Illumina’s TruSeq stranded kit, with polyA enrichment, 100 bp paired end sequencing of 83 total RNA samples from male mice’s (C57BL/6J/Ukj) colons at different ages: 3 (n = 16), 9 (n = 16), 15 (n = 16), 24 (n = 17), and 28 (n = 18) months.
Web link https://www.nature.com/articles/s41467-024-47316-2
 
Contributor(s) Olecka M, van Boemmel A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S
Citation(s) 38594255
Submission date Nov 16, 2023
Last update date Apr 15, 2024
Contact name Lena Best
E-mail(s) l.best@iem.uni-kiel.de
Organization name Christian-Albrechts-University Kiel
Department Institute of Experimental Medicine
Lab Kaleta Lab
Street address Michaelis-Straße 5
City Kiel
ZIP/Postal code 24105
Country Germany
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (83)
GSM7904486 Colon, 3 Months, Rep1 [3M.N1]
GSM7904487 Colon, 3 Months, Rep2 [3M.N2]
GSM7904488 Colon, 3 Months, Rep3 [3M.N3]
Relations
BioProject PRJNA1041390

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Supplementary file Size Download File type/resource
GSE248002_colon_RNA_gene_counts.tsv.gz 3.3 Mb (ftp)(http) TSV
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