|
| Status |
Public on Jul 01, 2024 |
| Title |
ATAC_muscle_WT_60h_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
muscle
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: muscle
cell line: C3H
cell type: muscle satellite cell
genotype: WT_60h
treatment: cell differentiation
|
| Treatment protocol |
The cells were treated with 5uM/ml SGC-CBP30 for 48h in the proliferation phase and 60h in the differentiation phase
|
| Growth protocol |
C3H cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The reaction system was incubated at 37 °C for 1 h followed immediately by purification with a QIAGEN MinElute PCR Purification Kit (QIAGEN, 28006)
Performed chromatin profiling with ATAC-Seq according to its latest protocol
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic
Trimmed sequence reads were mapped to Sscrofa11.1 genome
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the macs2. narrowPeak files were generated using MACS v2 with default settings.
Assembly: Sscrofa11.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Feb 02, 2023 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Xuan Wen Wang |
| E-mail(s) |
wwx840994072@gmail.com
|
| Phone |
13583396727
|
| Organization name |
Huazhong Agriculture University
|
| Street address |
No. 1 Shizishan Street
|
| City |
Wuhan |
| State/province |
Hubei Province |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (2) |
| GSE224380 |
Epigenetic study on CBP inhibiting differentiation of porcine muscle satellite cells (ATAC-Seq) |
| GSE224383 |
Epigenetic study on CBP inhibiting differentiation of porcine muscle satellite cells |
|
| Relations |
| BioSample |
SAMN33023114 |
| SRA |
SRX19261991 |
