|
| Status |
Public on Feb 26, 2021 |
| Title |
Sugen-Hypoxia 8 wks |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Total Lung
strain: Sprague-Dawley
genotype: Wild type
treatment: Sugen-Hypoxia
chip antibody: BML-SA210-0100, Enzo Life Sciences
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was conducted using pooled lung samples from SuHx rats at day4 , SuHx rats at 8weeks or normoxia control rats(day0) (3rats per group). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-AHR antibody(BML-SA210-0100, Enzo Life Sciences).
Libraries were prepared according to Illumina's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
pooled lung samples from 3 rats
|
| Data processing |
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings.
Only reads that pass illumina's pulify filter, align with no more than 2 mismatches, and map uniquely to the rn6 genome are used in the subsequent analysis.
Peaks are called using either MACS or SICER algorithms. MACS default cutoff is p value e-7 for narrow peaks and e^-1 for broad peaks,
and SICER default cutoff is FDR e^-10 with gap parameter of 600bp.
Genome_build: rn6
Supplementary_files_format_and_content: bw file
|
| |
|
| Submission date |
Nov 27, 2020 |
| Last update date |
Feb 27, 2021 |
| Contact name |
Takeshi Masaki |
| E-mail(s) |
tmasaki@ncvc.go.jp
|
| Phone |
81-6-6170-1070
|
| Organization name |
National Cerebral and Cardiovascular Center
|
| Department |
Vascular Physiology
|
| Street address |
6-1
|
| City |
Kishibe-Shinmachi,Suita |
| State/province |
Osaka |
| ZIP/Postal code |
564-8565 |
| Country |
Japan |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE162237 |
Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [ChIP-Seq] |
| GSE162245 |
RNA-seq analysis of Ahr-knockout rats of SuHx model. |
|
| Relations |
| BioSample |
SAMN16935360 |
| SRA |
SRX9596815 |
