|
| Status |
Public on Jul 04, 2019 |
| Title |
Temporal lobe cortex, HI hMeDIP 1 |
| Sample type |
SRA |
| |
|
| Source name |
temporal lobe cortex
|
| Organism |
Rattus norvegicus |
| Characteristics |
disease state: hypoxic-ischemic neonatal model of cerebral palsy
strain: SD
tissue: temporal lobe cortex
age: postnatal day 31
antibody: anti-5hmC antibody (Active Motif, Cat. No. 39769)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Brains were removed,and genomic DNA was isolated from the temporal cortex and immunoprecipitated by using an anti-5hmC antibody (Active Motif, United States, Cat. No. 39769).
Genomic DNA was sonicated and sequenced using the Illumina Hiseq2000 and Nextseq system (Illumina, United States) in accordance with the manufacturer’s instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: hMeDIP-Seq
FASTQ sequence files obtained were aligned to the reference genome of rats in UCSC databank (RGSC6.0/rn6) using Bowtie
Only unique non-duplicate reads were used for peak calling and annotation by HOMER (hypergeometric optimization of motif enrichment) software
DhMRs between control and HI rats were determined by comparing 5hmC peak levels by Model-based Analysis of ChIP-Seq (MACS) software
Genome_build: rn6
Supplementary_files_format_and_content: .bw
|
| |
|
| Submission date |
Jul 03, 2019 |
| Last update date |
Jul 07, 2019 |
| Contact name |
Yunpeng Zhang |
| E-mail(s) |
zhangyunpeng2019@163.com
|
| Phone |
+8618116335939
|
| Organization name |
Fudan university
|
| Department |
jinshan hospital
|
| Street address |
Longhang Road 1508 Jinshan distinct
|
| City |
Shanghai |
| ZIP/Postal code |
201500 |
| Country |
China |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE133787 |
Genome-wide alteration of 5-hydroxymethylcytosine in hypoxic-ischemic neonatal rat model of cerebral palsy |
|
| Relations |
| BioSample |
SAMN12211541 |
| SRA |
SRX6403208 |
