Epigenetic pacemaker (Sciuridae)

Knowledge graph centered on Epigenetic pacemaker (Sciuridae) with 24 nodes and 81 connections. Top connected: Marmota flaviventris, mark-recapture (Sciuridae), Parus major, winter survival, Ursus americanus.

Method synopsis

Development of species-specific epigenetic clocks using cross-mammalian methylation arrays and elastic-net penalized regression to predict chronological age from DNA methylation patterns.

Synthesized from method descriptions across 1 paper using this protocol.

Procedure from a recent peer-reviewed implementation

Steps below were extracted from the most recent peer-reviewed implementation of this protocol in the corpus — Hibernation slows epigenetic ageing in yellow-bellied marmots (2022), Nature Ecology & Evolution. Implementations in other papers (listed below) may differ.

1. DNA extraction and methylation profiling
   Genomic DNA was extracted using Qiagen DNeasy blood and tissue kit and quantified using NanoDrop. Custom methylation profiling was performed using mammalian methylation array probes targeting 31,388 CpG sites with corresponding response regions across mammals. The Infinium EPIC array platform was used with SesSaMe normalization.
   Quantities: 31,388 CpG sites analyzed across 149 samples from 73 females after quality controlDuration: Not specifiedConditions: Laboratory conditions
   Equipment: Qiagen DNeasy blood and tissue kit, NanoDrop, Infinium EPIC array, mammalian methylation array probes
2. Quality control and data filtering
   Used unsupervised hierarchical clustering to identify technical outliers. Removed putative platemap errors and averaged linkage hierarchical clustering based on inter-array correlation to identify technical outliers. Applied plate map error corrections and filtered out samples with insufficient DNA amounts.
   Quantities: 149 samples retained from initial 160 after quality control, 73 females representedDuration: Not specifiedConditions: Computational analysis
   Equipment: R software
3. Epigenetic clock model development
   Applied 10-fold cross validation using elastic-net penalization with α=0.5 to select CpG sites and minimize mean squared error between chronological and predicted ages. Used lasso penalties with equal weights for all CpG sites included in the model.

Typical Equipment

• Qiagen DNeasy blood and tissue kit
• NanoDrop
• Infinium EPIC array
• mammalian methylation array probes
• R software

Output Measurements

• epigenetic age
• chronological age prediction
• methylation levels

Papers Using This Protocol (1)

Species Studied With This Protocol