|
| Status |
Public on Jan 30, 2023 |
| Title |
MSC, control, F4170 [F4170-0] |
| Sample type |
SRA |
| |
|
| Source name |
mesenchymal stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mesenchymal stem cell
treatment: control
|
| Treatment protocol |
Paired samples of cells from each donor were treated with 1 ng/ml human recombinant transforming growth factor-beta2 (TGF-b2) for 72 hours
|
| Growth protocol |
Primary human mesenchymal stem cells were maintatined in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
PolyA selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36.
The trimmed reads were mapped to the EquCab 3.0 using the STAR aligner v.2.5.2b.
Unique hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Read count extraction and normalization were performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-deliniated text file containing normalized gene expression
|
| |
|
| Submission date |
Dec 07, 2022 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Alix Kay Berglund |
| E-mail(s) |
akberglu@ncsu.edu
|
| Organization name |
North Carolina State University
|
| Department |
Clinical Sciences
|
| Street address |
1060 William Moore Dr
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27607 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE220294 |
Gene expression in untreated and TGF-b2-treated human bone marrow-derived mesenchymal stem cells |
|
| Relations |
| BioSample |
SAMN32091762 |
| SRA |
SRX18523749 |
