|
| Status |
Public on Sep 29, 2022 |
| Title |
Mesenchymal stem cell, healthy donor 2,induction day 10 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
cell type: mesenchymal stem cells
genotype: WT
treatment: adipogenic differentiation
disease state: healthy
|
| Treatment protocol |
Adipogenic differentiation was induced for 10 days with 0.2 mM indomethacin (Sigma–Aldrich), 10 μg/mL insulin (Sigma–Aldrich), 0.5 mM 3-isobutyl-1-methylxanthine (Sigma–Aldrich) and 1 μM dexamethasone(Sigma–Aldrich)
|
| Growth protocol |
mesenchymal stem cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from MSCs using the Trizol (invitrogen) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit according to instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination, and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM/counts for each Sample
|
| |
|
| Submission date |
Sep 02, 2022 |
| Last update date |
Sep 29, 2022 |
| Contact name |
Zhenhua Liu |
| Organization name |
Zhujiang Hospital
|
| Department |
Spine surgery
|
| Lab |
orthopedic center
|
| Street address |
industry Avenue 253#
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510128 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE212613 |
Aberrant lncRNA–mRNA Expression Profile and Function Networks during the Adipogenesis of Mesenchymal Stem Cells from Patients with Ankylosing Spondylitis |
|
| Relations |
| BioSample |
SAMN30649086 |
| SRA |
SRX17408976 |
