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Sample GSM3931383 Query DataSets for GSM3931383
Status Public on Sep 16, 2021
Title sgBcl6_RNA-seq_rep1
Sample type SRA
 
Source name Skeletal muscle
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: muscle stem cells
age: post natal day 38
genotype: Pax7Cas9
Growth protocol 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 polyA RNA
Extraction protocol RNA from freshly isolated or culture muscle stem cells was harvested using Trizol reagent.
Purified mRNAs were fragmented and the cDNA were synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added. RNA-seq libraries were constructed according to the standard illumina pair-end sequencing procedure.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing 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 low-quality or duplication sequence are removed by a in-house scripts, then mapped to mm9 whole genome using tophat2 with parameters -a 8 -m 0 -I 500000 -p 20 -g 20 --library-type fr-firststrand --segment-mismatches 2 --no-coverage-search -r 50 --mate-std-dev 60
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
 
Submission date Jul 08, 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)
GSE133956 CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin [RNA-seq (myc&bcl6)]
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 SAMN12320269
SRA SRX6471689

Supplementary file Size Download File type/resource
GSM3931383_RNA_FISC_sgBcl6_br1_isoforms.fpkm_tracking.gz 1.3 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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