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Sample GSM5221120 Query DataSets for GSM5221120
Status Public on Apr 01, 2021
Title Aged_ENR3
Sample type SRA
 
Source name Dentate gyrus
Organism Mus musculus
Characteristics strain: C57BL/6JRj
tissue: Dentate gyrus
age: 17 months
Sex: Female
housing: Environmental enrichment
Treatment protocol Mice were housed in either standard cages or in an enriched environment.
Growth protocol Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.
Extracted molecule genomic DNA
Extraction protocol Dentate gyrus was micro-dissected from the brain.
Genomic DNA was isolated using the QIAamp DNA Micro Kit (QIAGEN) following the manufacturer’s manuals. RRBS libraries were prepared using the Premium RRBS Kit (Diagenode) and purified twice using Agencourt AMPure XP beads (Beckman Coulter; 1X bead volume). Quality and concentration of RRBS libraries were determined using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical) and a fragment analyzer with capillary size of 33 cm (Advanced Analytical).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina NextSeq 500
 
Description Methylated cytosines converted to uracil by treatment with sodium bisulfite
Data processing Fastq reads were trimmed using Trim Galore 0.4.0 and the function Cutadapt 1.8.1. To remove cytosines that were filled in during ends preparation, an additional 2 bp were cut off from every sequence with detected adapter.
Trimmed reads were mapped against mm10 using Bismark 0.16.1
Base calling was performed using MethylKit 1.5.2.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation percentages of cytosines for all samples. Comma-delimited text file exported from Methylkit.
 
Submission date Mar 31, 2021
Last update date Apr 02, 2021
Contact name Gerd Kempermann
E-mail(s) gerd.kempermann@dzne.de
Organization name German Center for Neurodegenerative Diseases (DZNE)
Street address Tatzberg 41
City Dresden
State/province Saxony
ZIP/Postal code 01307
Country Germany
 
Platform ID GPL19057
Series (2)
GSE138368 Environmental enrichment restores a young DNA methylation landscape in the aged mouse hippocampus
GSE171236 Environmental enrichment restores a young DNA methylation landscape in the aged mouse hippocampus [Experiment 3]
Relations
BioSample SAMN18572574
SRA SRX10489291

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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