Methylation studies in naked mole rat. Part 1

An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues of the naked mole rat We generated DNA methylation data from n=289 tissues. All tissues except for skin biopsies and blood were obtained from frozen tissue collection that were euthanized for other studies. Skin biopsies (2 mm punch) were collected from the backs of the animals under local anesthesia. Blood samples were collected from the tails. The n=3 induced pluripotent stem cells from NMR were generated as described in (Tan et al 2017., PMID: 29107597). As control set for the iPS study, we used n=3 fibroblasts samples. Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue kit and quantified using Nanodrop and Qubit.als N=289 DNA samples from 13 sources of DNA: adipose, blood, cerebellum, cerebral cortex, fibroblast, heart, induced pluripotent stem cells, kidney, liver, lung, muscle, skin, spleen. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium The characteristics: Queen pertains to female naked mole rats. Queen=yes indicates that the female is a breeding queen. Queen=no indicates that the animal is a non-breeding female. NA=not applicable (e.g. male) or unknown. The characteristics: ConfidenceInAgeEstimate with numeric value between 0 and 100. It indicates the confidence in the accuracy in the age estimate. This value was assigned by the team of investigators. It is based on their subjective confidence in the accuracy of the record when it comes to the chronological age at the time of samle collection. A value of 100 was chosen for samples whose birthday and death date was accuratly kown. We only used samples with a confidence of 90 or higher when building or evaluating DNA methylation based age estimators or when conducting epigenome wide association studies of chronological age. The characteristics: Age represents chronological/calendar age of the animal at the time of sample collection. Age is in units of years.