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SRX7031909: Bisulfite ddRADseq of Peromyscus maniculatus gracilis: adult male skull
1 ILLUMINA (Illumina HiSeq 2500) run: 980,585 spots, 217.4M bases, 657.4Mb downloads

Design: Bisulfite ddRADseq
Submitted by: University of Michigan
Study: Bisulfite ddRAD sequencing of historic Peromyscus museum specimens
show Abstracthide Abstract
In this study, we develop and test methods to characterize cytosine methylation in dried skulls up to 76 years old. Using a combination of ddRAD and bisulfite treatment, we characterized patterns of cytosine methylation in two species of deer mouse (<i>Peromyscus spp.</i>) collected in the same region in Michigan in 1940, 2003, and 2013-2016. We successfully estimated methylation in specimens of all age groups, though older specimens yielded less data and showed greater interindividual variation in data yield than newer specimens. Global methylation estimates were reduced in the oldest specimens (76 years old) relative to the newest specimens (1-3 years old), which may reflect <i>post mortem</i> hydrolytic deamination. Methylation was reduced in promoter regions relative to gene bodies and showed greater bimodality in autosomes relative to female X chromosomes, consistent with expectations for methylation in mammalian somatic cells. Our work demonstrates the utility of historic specimens for methylation analyses, as with genomic analyses; however, studies will need to accommodate the large variance in the quantity of data produced by older specimens.
Sample: MZ11328
SAMN13071862 • SRS5552018 • All experiments • All runs
Library:
Name: MZ11328
Instrument: Illumina HiSeq 2500
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: Restriction Digest
Layout: PAIRED
Runs: 1 run, 980,585 spots, 217.4M bases, 657.4Mb
Run# of Spots# of BasesSizePublished
SRR10321086980,585217.4M657.4Mb2019-11-17

ID:
9237803

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