|
| Status |
Public on Jan 16, 2024 |
| Title |
ctrl2 |
| Sample type |
SRA |
| |
|
| Source name |
human MSCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human umbilical cord MSCs
agent: ctrl
|
| Treatment protocol |
MSCs were treated with rhIL-10 or not for 8 h.
|
| Growth protocol |
Human umbilical cord mesenchymal stem cells (MSC) were culture in MEM-α medium, 10% fetal bovine serum, human FGF (20 ng/mL) and human EGF (20 ng/mL).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from MSCs were treated with rhIL-10 or not were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava 2.19 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample
|
| |
|
| Submission date |
Aug 14, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Jiajia Wang |
| E-mail(s) |
wangjiajia3301@zju.edu.cn
|
| Organization name |
Zhejiang University
|
| Lab |
GLP_lab
|
| Street address |
866 Yuhangtang Road
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE240755 |
The initiating IL-10 production dominates the therapy of mesenchymal stem cell scaffold in spinal cord injury |
|
| Relations |
| BioSample |
SAMN36978201 |
| SRA |
SRX21356273 |
