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Series GSE174777 Query DataSets for GSE174777
Status Public on Oct 18, 2021
Title Methylation studies in naked mole rat. Part 1
Platform organisms Homo sapiens; Mus musculus; Rattus norvegicus
Sample organism Heterocephalus glaber
Experiment type Methylation profiling by array
Summary 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
 
Overall design 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.
Web link https://doi.org/10.1038/s43587-021-00152-1
 
Contributor(s) Horvath S, Gorbunova V, Seluanov A
Citation(s) 37563227, 38848365
Submission date May 20, 2021
Last update date Jun 26, 2024
Contact name Steve Horvath
E-mail(s) shorvath@altoslabs.com
Organization name University of California, Los Angeles
Department Human Genetics
Lab Horvath
Street address 695 Charles E. Young Drive South, Box 708822
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
 
Platforms (1)
GPL28271 Illumina HorvathMammalianMethylChip40 BeadChip
Samples (289)
GSM5327624 Sample1.Naked mole rat.203203210200_R01C01
GSM5327625 Sample2.Naked mole rat.203203210200_R02C01
GSM5327626 Sample3.Naked mole rat.203203210200_R03C01
Relations
BioProject PRJNA731507

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
GSE174777_RAW.tar 215.7 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table
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