|
| Status |
Public on Jun 16, 2016 |
| Title |
Lesioned/L-DOPA Treated 5 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal Striatum
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: Brain/Dorsal Striatum
age: 120 days
genotype: Wild Type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Rats were given a unilateral dopaminergic lesion to the left medial forebrain bundle with 6-OHDA to destroy at least 90% of TH positive axons. Animals were allowed to recover for 3 weeks and then given daily injections of L-DOPA (6 mg/kg) for seven days to establish stable dyskinesia. Animals were sacked 3 hrs following the final L-DOPA injection and the dorsal striatum was immediately dissected and flash frozen
One μg of gDNA sample was used for library construction. Bisulfite converted DNA libraries were produced and adaptor ligated, and 50 bp single-end reads were sequenced on an Illumina HiSeq-2500 following library QC and analyzed using Illumina Casava 1.8.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Bisulfite Converted Genomic DNA
Lesioned/L-DOPA Treated
|
| Data processing |
Bisulfite conversion efficiency was greater that 98% for all of the samples and we obtained an average of 68 million reads per library. Quality control on raw reads was performed with FastQC (version 0.10.1, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc), and adaptor trimming and removal of trimmed reads shorter than 20 bp was performed with Trim Galore (version 0.3.7, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore).
Trimmed reads were mapped to the UCSC Rattus norvegicus rn5 genome with the methylation-aware mapper bismark (version 0.13.0). Samtools (version 0.1.19–96b5f2294a) used to sort SAM files produced by bismark and de-duplicate reads. SAM files were analyzed using MethylKit (version 0.9.2) in R (Akalin et al., 2012).
Genome_build: Rn5
Supplementary_files_format_and_content: tab delimited text files containing CpG methylation info for all analyzed cytosines including chromosome, base pair, strand, coverage, frequency of methylated cytosine, frequency of bisulfite coverted cytosine to thymidine
|
| |
|
| Submission date |
Jun 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
David Figge |
| E-mail(s) |
figgeda@uab.edu
|
| Organization name |
University of Alabama-Birmingham
|
| Department |
Neurology
|
| Street address |
1719 6th Ave. S, CIRC 520
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE83385 |
Dynamic DNA Methylation Regulates Levodopa-Induced Dyskinesia |
|
| Relations |
| BioSample |
SAMN05253210 |
| SRA |
SRX1847169 |
