|
| Status |
Public on Sep 16, 2021 |
| Title |
HiC_KO_Q_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Skeletal muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Quiescent muscle stem cell
age: post natal day 38
genotype: Pax7Cas9
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by QuickExtract (Epicentre) solution.
DNA fragments containing biotin were enriched by Dynabeads MyOne Streptavidin C1 (Invitrogen 65001) for 15min at room temperature, followed by end repairing, adaptor ligation and PCR amplification
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
KO_QSC_HiC_br2
|
| Data processing |
The in-situ Hi-C data was processed following a standard pipeline Hi-C-Pro. Briefly, the reads were aligned to reference genome (mm9) in two steps: global alignment was first performed for all pair-end reads; unaligned reads were then trimmed by restriction enzyme and aligned again.
All aligned reads were then merged together to assign to restriction fragment. In this step, invalid fragments (dangling end, self-cycle etc.) were discarded and PCR duplications were removed for each biological replicate separately.
At last, all validate pairs were merged for each condation and then normalized by read depth using HOMER followed by ICE matrix balancing to further get interaction matrix.
Genome_build: mm9
|
| |
|
| Submission date |
Sep 13, 2020 |
| 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) |
| 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 |
| GSE157872 |
CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [Hi-C] |
|
| Relations |
| BioSample |
SAMN16121589 |
| SRA |
SRX9112715 |
