|
| Status |
Public on Mar 20, 2024 |
| Title |
pbsc, h3k4me1, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
muscle
|
| Organism |
Bos taurus |
| Characteristics |
tissue: muscle
cell type: satellite cells
treatment: growth medium
|
| Treatment protocol |
Bovine satelltie cells cultured in growth medium were induced to differentiate into myofibers 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 up to 10 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed to release nuclei; nuclei were sonicated; and histone-DNA complexes were immunoprecipitated with specific antibodies.
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 NovaSeq 6000 |
| |
|
| 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
Assembly: BosTau 9
Supplementary files format and content: peak files in BigWig, no peak files for Input samples
|
| |
|
| Submission date |
Jan 16, 2024 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Honglin Jiang |
| E-mail(s) |
hojiang@vt.edu
|
| Phone |
540-231-1859
|
| Organization name |
Virginia Tech
|
| Department |
School of Animal Sciences
|
| Street address |
Litton Reaves Hall
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE253395 |
Chromatin profiling reveals many transcriptional regulators of proliferation and differentiation of bovine satellite cells |
|
| Relations |
| BioSample |
SAMN39464055 |
| SRA |
SRX23254890 |
