|
| Status |
Public on Sep 16, 2021 |
| Title |
Ctrl_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 |
SAMN12320273 |
| SRA |
SRX6471685 |
