|
| Status |
Public on Sep 16, 2021 |
| Title |
ASC_ChIP-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Skeletal muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Actiavetd muscle stem cells
age: 6-8 weeks
genotype: Pax7-nGFP
|
| Growth protocol |
Freshly isolated muscle stem cells were cultured in growth medium containing F10, 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% pen/strep for 24h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from freshly isolated or activated muscle stem cells were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies.
ChIP-seq libraries were constructed closely according to the standard illumina pair-end or single-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 HiSeq 1500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie2 v2.2.3 with default parameters
Duplication reads are removed by picard with default parameters,and then merged alignment files are used to call peaks by MACS2 with q-value equal to 0.01
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files are generateed by homer
|
| |
|
| Submission date |
Jul 19, 2019 |
| Last update date |
Sep 16, 2021 |
| Contact name |
Yingzhe Ding |
| E-mail(s) |
1155068845@link.cuhk.edu.hk
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
Chemical Pathology
|
| Street address |
Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.
|
| City |
Hong Kong |
| State/province |
Shatin NT. |
| ZIP/Postal code |
999077 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE134524 |
CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [ChIP-seq] |
| GSE134529 |
CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin |
|
| Relations |
| BioSample |
SAMN12320303 |
| SRA |
SRX6471694 |
