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Sample GSM3955145 Query DataSets for GSM3955145
Status Public on Sep 16, 2021
Title FISC_ChIP-seq_rep2
Sample type SRA
 
Source name Skeletal muscle
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Freshly isolated 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 SAMN12320266
SRA SRX6471692

Supplementary file Size Download File type/resource
GSM3955145_FISC_br2_tr1.bedGraph.gz 57.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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