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Sample GSM3955179 Query DataSets for GSM3955179
Status Public on Sep 16, 2021
Title MyoD_dual_deep seq_rep3
Sample type SRA
 
Source name Skeletal muscle
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Freshly isoalted muscle stem cell
age: post natal day 38
genotype: Pax7Cas9
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted by QuickExtract (Epicentre) solution.
Genomic DNAs from AAV9-sgRNA infected satellite cells were amplified using Q5 High-Fidelity 2× Master Mix (NEB). PCR products were purified through QIAQuick PCR purification kit (Qiagen) and subjected to library preparation using NEBNext® Ultra™ II DNA Library Preparation Kit (NEB).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Data processing Library strategy: Deep-seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and reads without primer or low-quality sequence are removed,then mapped to mm9 and conduct editting pattern using CRISPResso with parameter -w 15 -p 12 --save_also_png --keep_intermediate
Genome_build: mm9
Supplementary_files_format_and_content: folder(with all CRISPResso2 output files inside)
 
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)
GSE134527 CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [Deep-seq(single vs dual)]
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 SAMN12320291
SRA SRX6471705

Supplementary file Size Download File type/resource
GSM3955179_dual_sgRNA_4_rep3.zip.gz 6.4 Mb (ftp)(http) ZIP
GSM3955179_dual_sgRNA_c_rep3.zip.gz 4.4 Mb (ftp)(http) ZIP
GSM3955179_dual_sgRNA_paired_rep3.zip.gz 9.6 Mb (ftp)(http) ZIP
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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