|
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).
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|
|
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.
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|
|
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 |