|
| Status |
Public on Jun 02, 2017 |
| Title |
DM_48hr_H23_KO_H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: myoblasts
developmental stage; time in differentiation medium: DM 48 hours
antibody: H3K27ac (Abcam ab4729)
|
| Treatment protocol |
C2C12 myoblasts were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep)
|
| Growth protocol |
C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatins from myoblasts and myotubes were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies
ChIP-seq libraries were constructed closely according to the standard illumina pair-end ChIP-seq procedure
After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads by ChIP-seq were mapped to mm9 genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 (v2.1.0), a p-value of 10^-4 was used as the cutoff
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation. Overlapping analysis was performed using in-house programs and the maximum distance limitation was set to 1000bp.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS, scores represent -10*log(p)
|
| |
|
| Submission date |
Jan 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiajian Zhou |
| E-mail(s) |
zhoujj2013@gmail.com
|
| Organization name |
Southern Medical University
|
| Department |
Dermatology Hospital
|
| Street address |
No. 2 Lujing Road, Yuexiu District,
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
NA |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE93916 |
MyoD and FoxO3 mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation |
|
| Relations |
| BioSample |
SAMN06249370 |
| SRA |
SRX2510498 |
