|
| Status |
Public on Feb 06, 2022 |
| Title |
2dU2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse MuSCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: FACS-sorted MuSCs from Pax7-ZsGreen mice's hindlimb
strain: Pax7-ZsGreen
treatment: 2-day culturing, uncompressed
|
| Treatment protocol |
Compression pillar was appplied to the cell culture 2 days post-culturing (for the compressed cells). Others were untreated
|
| Growth protocol |
FACS-sorted MuSCs werecultrued on the Matrigel-fibronactin-coated plastic-bottom plate, with growth media 1% PS, 0.01% of Fungin, Plasmocin, 0.1% of chicken embryo extract, 10 ng/mL FGF, 5% of HS and 20% of FBS in DMEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol was directly added to the cell culture, after removing the media and compression pillar (for the compressed samples)
Libraries were prepared according to Illumina's instructions. Purified RNA samples were reverse-transcribed to cDNA and amplified using SMART-seq v4 Ultra Low Input Kit for Sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumnia's bcll2fastq/2.20.0 was used to generate Fastq files. Default parameters were used.
Reads were processed using the nf-core RNA-seq v1.4.2 bioinformatics pipeline (https://nf-co.re/rnaseq/1.4.2). (Mapped with mm10 genome and annotated with GENCODE M23)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Feb 03, 2022 |
| Last update date |
Feb 07, 2022 |
| Contact name |
Jiaxiang Tao |
| E-mail(s) |
taojiaxiangjit9@gmail.com
|
| Phone |
4102415039
|
| Organization name |
Georgetown University
|
| Department |
Oncology
|
| Street address |
3970 Reservoir Road NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20007 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE196101 |
Mechanical Compression Creates a Quiescent Muscle Stem Cell Niche |
|
| Relations |
| BioSample |
SAMN25643178 |
| SRA |
SRX14039232 |
