|
| Status |
Public on Jul 06, 2022 |
| Title |
MSC, control, Horse D |
| Sample type |
SRA |
| |
|
| Source name |
mesenchymal stem cell
|
| Organism |
Equus caballus |
| Characteristics |
cell type: mesenchymal stem cell
treatment: Control
|
| Treatment protocol |
Half of the bone marrow from each horse was treated with 1 ng/ml human recombinant transforming growth factor-beta2 (TGF-b2) from initial isolation through passage 3 or 4
|
| Growth protocol |
Primary equine bone marrow-derived mesenchymal cells were maintained 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 |
| |
|
| Description |
D0
|
| 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: EquCab 3.0
Supplementary files format and content: tab-deliniated text file containing normalized gene expression data
|
| |
|
| Submission date |
Jul 03, 2022 |
| Last update date |
Jul 06, 2022 |
| 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 |
GPL21941 |
| Series (1) |
| GSE207394 |
Gene expression in untreated and TGF-b2-treated equine bone marrow-derived mesenchymal stem cells |
|
| Relations |
| BioSample |
SAMN29485196 |
| SRA |
SRX16005230 |
