|
Status |
Public on Jan 16, 2024 |
Title |
ctrl1 |
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 |
SAMN36978202 |
SRA |
SRX21356272 |