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Series GSE174778 Query DataSets for GSE174778
Status Public on Oct 18, 2021
Title Methylation studies in mole rats. Part 2
Platform organisms Homo sapiens; Mus musculus; Rattus norvegicus
Sample organisms Georychus capensis; Heterocephalus glaber; Fukomys damarensis
Experiment type Methylation profiling by array
Summary An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues of 3 species of mole rats: Cape mole rat (Georychus capensis), Damaraland mole rat (Cryptomys damarensis), Naked mole rat (Heterocephalus glaber). We generated DNA methylation data from n=94 tissues from 3 species: Cryptomys damarensis (n=10), Georychus capensis (n=6), Heterocephalus glaber (n=78). All tissues ewere obtained from frozen tissue collection that were euthanized for other studies. Kidney (n=6), liver (n=61), skin (n=27).
The tissues used in this study were obtained from post-mortem specimens from animals free from disease in compliance. Sample collection was from post-mortem material. Tissue samples were snap frozen in liquid nitrogen following dissection and transferred for storage at -80ºC. Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue kit and quantified using Nanodrop and Qubit.als
 
Overall design Genome annotations of the mammalian methylation 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.
 
Contributor(s) Horvath S, Faulkes C
Citation(s) 37563227
Submission date May 20, 2021
Last update date Sep 21, 2023
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 (94)
GSM5327913 Sample1.Naked mole rat.203203210214_R01C01
GSM5327914 Sample2.Naked mole rat.203203210214_R02C01
GSM5327915 Sample3.Naked mole rat.203203210214_R03C01
Relations
BioProject PRJNA731509

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
GSE174778_RAW.tar 70.7 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table
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