|
| Status |
Public on Aug 02, 2017 |
| Title |
2190 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Fischer 344
tissue: medial prefrontal cortex
age: Aged
age impairment: Impaired
rat identifier: 2190
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rats were anesthetized with isoflurane, decapitated and the brain was rapidly removed. The prelimbic and infralimbic mPFC was collected. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC. Genomic DNA was isolated with the DNeasy Blood & Tissue kit (Qiagen, catalog number: 69504). Bisulfite conversion was performed with the EZ DNA Methylation-Direct kit (Zymo Research, catalog number: D5020).
Whole-genome bisulfite sequencing (WGBS) libraries were constructed with the Illumina TruSeq DNA Methylation kit (Illumina, catalog number: EGMK91324). Following size selection and amplification, the concentration of each library was quantified using the Qubit dsDNA HS Assay and size distribution was evaluated with the High Sensitivity D1000 Screen Tape in the Tapestation system (Agilent Technologies).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Bisulfite converted
Processed data file: Aging-Young-CG-mat.csv
Processed data file: Aging-Young-CHG-mat.csv
Processed data file: Aging-Young-CHH-mat.csv
Processed data file: AI-AU-CG-mat.csv
Processed data file: AI-AU-CHG-mat.csv
Processed data file: AI-AU-CHH-mat.csv
|
| Data processing |
WGBS data was analyzed using the DMAP2 pipeline available at the University of Florida high performance computer clusters. Briefly, quality assessment and trimming of fastq files were performed with FastQC and trimmomatic. Alignment to the rn5 genome was executed with BSMAP (default parameters). DNA methylation calling at CpG, CHG and CHH was performed with the ‘cscall’ program (mindepth=5; minsamples=3 for minimum coverage of 15x for each site in each group).
Annotation was performed using the Rnor_5.0.78.gtf file, and all sites were annotated according to promoters and gene body (exons and introns) regions using the "genediffmeth" program at the university's clusters.
Genome_build: rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *.csv: Comma-separated values files contain the DNA methylation ratios per biological replicate for each site (indicated by chromosome number and coordinate).
|
| |
|
| Submission date |
Apr 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas C Foster |
| E-mail(s) |
foster1@ufl.edu
|
| Organization name |
University of Florida-McKnight Brain Institute
|
| Department |
Neuroscience
|
| Lab |
Foster
|
| Street address |
1149 Newell Drive Bldg 59
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32611 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE97612 |
DNA Methylation of Synaptic Genes in the Prefrontal Cortex is Associated with Aging and Age-Related Cognitive Impairment |
|
| Relations |
| BioSample |
SAMN06706334 |
| SRA |
SRX2732286 |
