|
| Status |
Public on Dec 23, 2021 |
| Title |
ChIP1 BD bovine satellite cells |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle
|
| Organism |
Bos taurus |
| Characteristics |
breed: Angus-crossbred
cell type: muscle satellite cells
treatment: before differentiation
antibody: H3K27ac
|
| Treatment protocol |
Bovine satelltie cells cultured in growth medium were induced to differentiate into myotubes by replacing the growth medium with differentiation medium containing 2% horse serum.
|
| Growth protocol |
Bovine satellite cells were cultured in growth medium containing 10% fetal bovine serum for about a week.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed to release nuclei; nuclei were sonicated; and histone-DNA complexes were immunoprecipitated with H3K27ac antibody.
ChIP-seq libraries were prepared using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs), according to the supplier’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adapters were trimmed using Trimmomatic
Trimmed sequencs were aligned to the bovine genome assembly using Hisat2
The aligned reads were sorted and merged using SAMtools
Peak calling of the aligned reads was made using MACS3 (3.0.0a5)
Genome_build: ARS-UCD 1.2 BosTau 9
Supplementary_files_format_and_content: peak files in BigWig
|
| |
|
| Submission date |
Jul 09, 2021 |
| Last update date |
Dec 23, 2021 |
| Contact name |
Honglin Jiang |
| E-mail(s) |
hojiang@vt.edu
|
| Phone |
540-231-1859
|
| Organization name |
Virginia Polytechnic Institute and State University
|
| Department |
Animal and Poultry Sciences
|
| Street address |
3130 Litton Reaves Hall
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL19172 |
| Series (1) |
| GSE179821 |
Identification of H3K27ac-marked enhancers in bovine satellite cells during differentiation |
|
| Relations |
| BioSample |
SAMN20153125 |
| SRA |
SRX11397260 |
