Heterocephalus glaber
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA70723 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Heterocephalus glaber Transcriptome or Gene expression
| PRJNA283581 | ENA
Project description:Transcriptome sequencing of naked mole rat, Heterocephalus glaber
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Project description:Heterocephalus glaber whole genome sequencing and assembly
| PRJNA763403 | ENA
Project description:Heterocephalus glaber strain:Stockholm Genome sequencing and assembly
| PRJNA825530 | ENA
Project description:Heterocephalus glaber isolate:MEF-2018 Genome sequencing and assembly
| PRJNA505051 | ENA
Project description:The naked mole-rat, Heterocephalus glaber (NMR), the longest-lived rodent with a maximum possible lifespan exceeding 33 years, is emerging as an important non-model organism for the study of longevity and healthspan. As such it is of significance and interest in the study of biomarkers for ageing in mammals. Recent breakthroughs in this field have indicated that ‘epigenetic clocks’ based on the temporal accumulation of DNA methylation at specific genomic sites can enable accurate age estimates for tissues across the lifespan of an individual. Here, we validate the hypothesis of an epigenetic clock in NMRs, and create a method for predicting the age of naked mole-rats based on changes in methylation of targeted CpG sites in regions known as ageing-associated differentially methylated positions (aDMPs). In the discovery phase, we performed a targeted analysis of 51 different CpGs in 24 different NMR livers spanning an age range from 39 weeks to 1,144 weeks. Of these 51 different sites, 23 were found to be significantly associated with age (p < 0.05). We then built a predictor of age using the 23 sites that showed an association with age. To test the accuracy of this model, we predicted age in an additional test set of 19 different livers spanning an age range 43 to 1,196 weeks. Our model was able to successfully predict age in the test with a root mean squared error (RMSE) of 166.11 weeks. We also profiled a 20 skin samples with the same age range and found a striking correlation between the predicted age of these samples versus their actual age (R=0.93). However, this correlation when compared to the liver samples showed a lower predicted age than actual age, suggesting that skin tissue ages slower than the liver in NMRs. Finally, we have produced freely available software tool that will take in raw sequencing data and produce an age prediction for new NMR samples. Our model will enable the prediction of age in wild caught naked mole-rats and captive animals of unknown age, and will be invaluable for further mechanistic studies of mammalian ageing.
2020-04-07 | GSE137957 | GEO
Project description:Chromosome-length, trio-binned, diploid genome assembly of the naked mole-rat (Heterocephalus glaber) by integrating Nanopore long-read genome sequencing, 10X short read genome sequencing, and Hi-C sequencing.
| PRJEB52763 | ENA