|
| Status |
Public on Mar 31, 2018 |
| Title |
d-2d-TRT-psc-1_H7K7MCCXY_L4 |
| Sample type |
SRA |
| |
|
| Source name |
Muscle satellite cells
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: Muscle satellite cells
developmental stage: differentiation
time: 48 hours
untreated and treated poly (i: c): treated
|
| Treatment protocol |
After 24h of culturing, porcine satellite cells were treated with 10 µg/mL of poly (I:C) within 12h and untreated PSCs as control. Next, the cells were washed once with PBS and entered into differentiation stages. The triplication of each sample at 4-time points, including0h and 12h of proliferation stage, at 24h and 48h of differentiation stage, was collected from poly (I:C) stimulation.
|
| Growth protocol |
Porcine satellite cells (PSCs) were isolated from the hindlimb muscle of 5-days-old male piglet.After isolating, PSCs were seeded at a density of (specific density/cm2), in 6-well plates pre-coated with gel, and incubated at 37°C under 5%CO2overnight with growth medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At each time point, the poisoned effect of PSCs was harvested by TRIzol 0.25%.
A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The quality of RNA sequence data was controlled using FastQC software and trimmed using the Trimmomatic tool
The trimmed adapters and purified sequences were mapped and identified based on Ensembl Sus scrofa 11.1.90 set GTF annotation genome utilizing HISAT2
Stringtie was used to estimate gene expression and transcript levels via FPKM (fragments per kilobase of transcript per million mapped fragments) approach
Genome_build: Ensembl Sus scrofa 11.1.90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Mar 30, 2018 |
| Last update date |
Apr 11, 2018 |
| Contact name |
Thuy Nhien Tran Thi |
| E-mail(s) |
thuynhien1908@gmail.com
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Shizishan
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE112527 |
Gene expression profiling of porcine skeletal muscle satellite cells after challenge with poly I:C |
|
| Relations |
| BioSample |
SAMN08822353 |
| SRA |
SRX3866276 |
