|
| Status |
Public on Aug 16, 2023 |
| Title |
SON_M125_3 |
| Sample type |
SRA |
| |
|
| Source name |
Supraoptic Nucleus
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Supraoptic Nucleus
Sex: Male
strain: Sprague Dawley
treatment: Age - 125 days old
|
| Treatment protocol |
Rats were grown to the ages of 35 days old or 125 days old prior to tissue collection.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rats were anesthetized with isoflurane and euthanized via transcardial perfusion with PBS. Brains were serial sectioned via vibratome and a tissue puncher was used to collected the supraoptic nucleus, which were immediately flash frozen by liquid nitrogen.
Genomic DNA was collected by ethanol precipitation. In brief, frozen tissue was ground under liquid nitrogen, and lysed with buffer ATL (Qiagen). DNA was isolated via phenol:chloroform: isoamyl alcohol and cintrifuged. DNA was washed and precipitated with 70% ethanol and the resuting DNA pellet was resuspended in buffer EB (Qiagen).
DNA was fragmented using a Covaris g-TUBE (Covaris). Libraries were prepared using the Oxford Nanopore Ligation Sequencing Kit (Oxford).
Other - long-read DNA sequencing nanopore
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
GridION |
| |
|
| Data processing |
Fastq reads were indexed using Nanopolish (v0.14.0).
Reads were aligned to rn7 assembly using minimap2 (v2.24) and indexed with Samtools (v1.6).
CpG methylation calling was performed using Nanopolish.
Methylation frequency was determined by the "calculate_methylation_frequency.py" script provided by Nanopolish.
Assembly: rn7
Supplementary files format and content: Text file of tab-separated values (.tsv) of called methylation values.
|
| |
|
| Submission date |
May 03, 2023 |
| Last update date |
Aug 16, 2023 |
| Contact name |
John Andrew Watt |
| E-mail(s) |
john.watt@und.edu
|
| Phone |
701-777-6225
|
| Organization name |
University of North Dakota
|
| Department |
Biomedical Sciences
|
| Lab |
Watt
|
| Street address |
504 Nth Hameline St
|
| City |
Grand Forks |
| State/province |
North Dakota |
| ZIP/Postal code |
58203 |
| Country |
USA |
| |
|
| Platform ID |
GPL33374 |
| Series (2) |
| GSE231615 |
Age-dependent DNA methylation characterization of the rat supraoptic nucleus (Methylation) |
| GSE231617 |
Transcriptome and Methylome of the Supraoptic Nucleus Provides Insights into the Age-dependent Loss of Neuronal Plasticity |
|
| Relations |
| BioSample |
SAMN34572387 |
| SRA |
SRX20211056 |
