|
| Status |
Public on Jul 13, 2018 |
| Title |
Norm2 MeDIP seq |
| Sample type |
SRA |
| |
|
| Source name |
skin tissue from nonirradiated area
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: skin
Sex: male
age: 4 weeks
|
| Treatment protocol |
Male Sprague-Dawley (SD) rats (4 weeks old) were irradiated with a single 45-Gy dose of irradiation was administered to the treatment area at a rate of 750 cGy/min using a 6-MeV electron beam accelerator (Clinac 2100EX, Varian Medical Systems, Inc., CA). The NC-group indicates non-irradiated skin areas.
|
| Growth protocol |
SPF condition for the growth of SD rats.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using phenol–chloroform, precipitated with ethanol and sonicated to 100–500 bp using Bioruptor (Diagenode). Sonicated DNA was end repaired, A tailed, and ligated to adapters by using NEBNext® Ultra™ DNA Library Prep Kit (NEB). Then, MeDIP was performed with a monoclonal antibody against 5-methylcytosine by following the standard manufacturer’s protocol (Active Motif).
MeDIP DNA libraries were quantified using Quant-iT PicoGreen dsDNA Kits (Life Technologies), and subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality reads were generated. Then these high quality reads were aligned to rat reference genome (UCSC RN5) using bowtie2 software (v2.2.4) with default parameters.
Peak calling was performed with MACS software (v1.4.3). Differentially methylated regions (DMRs) were identified by diffReps software (v1.55.4).The enriched methylated peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
GO and KEGG Pathway analysis were performed on the peak-associated genes or differentially methylated region-associated genes.
Genome_build: RN5
Supplementary_files_format_and_content: excel format: enriched peaks
|
| |
|
| Submission date |
Jul 06, 2018 |
| Last update date |
Jul 13, 2018 |
| Contact name |
zhang shu yu |
| E-mail(s) |
zhang.shuyu@hotmail.com
|
| Phone |
15851417273
|
| Organization name |
Soochow University
|
| Department |
soochow university
|
| Lab |
radiation
|
| Street address |
No. 199, Ren'ai Road
|
| City |
suzhou |
| ZIP/Postal code |
215123 |
| Country |
China |
| |
|
| Platform ID |
GPL22396 |
| Series (2) |
| GSE116747 |
DNA methylation analysis of radiation-induced skin fibrosis of rats |
| GSE116748 |
RNA-seq, YY1 ChIP-seq and MeDIP-seq of radiation-induced skin fibrosis of rats |
|
| Relations |
| BioSample |
SAMN09623824 |
| SRA |
SRX4349353 |
