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Sample GSM4777745 Query DataSets for GSM4777745
Status Public on Sep 16, 2021
Title HiC_KO_Q_rep1
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_br1
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 SAMN16121590
SRA SRX9112714

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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