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| Status |
Public on Dec 02, 2021 |
| Title |
The effect of FBS and cyclic mechanical stretch on serum starved mesenchymal stem cells |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Cyclic mechanical stretch (CMS) promoted proliferation of serum starved mesenchymal stem cells (MSCs) by inhibiting miR-337 expression, similar to FBS. In order to reveal the underlying mechanisms of both CMS and FBS on MSC activation, as well as the regulatory role of miR-337, this research performed high-throughput RNA sequencing (RNA-seq) on MSCs isolated from both wild-type (ET)- and miR-337 knockout- (miR-337-/-) rats.
Methods: MSCs isolated form 2-month-old wild-type (WT) and miR-337 knockout (-/-) rats and cultured in vitro to passage 3. After serum starvation for 8h, MSCs were treated with FBS or 10% CMS for another 24h before deep sequencing in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level.
Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample. We identified 2472 differentially expressed genes (DEGs) between CMS-stimulated vs. SSt conditions, 2468 DEGs FBS-treated vs. SSt groups. However, only 97 DEGs were identified between CMS and FBS groups, indicating that CMS and FBS groups are more similar to each other and both CMS and FBS groups are quite different from the SSt group. Analysis of DEGs between CMS- or FBS-treated and SSt -treated group revealed that CMS and FBS stimulation activated similar biological processes, of which, PI3K-Akt-mTOR pathway was highly enriched. However, PI3K-Akt-mTOR pathway was not enriched in miR-337-/- MSCs, indicating constitutive activation of this pathway.
Conclusions: Our RNA-seq data revealed that both CMS and FBS activates quiescent MSCs through regulating similar genes and pathways. miR-337 is one of the main factors that regulate MSC activation by targeting PI3K-Akt pathway.
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| Overall design |
MSCs isolated from WT and miR-337-/- rats underwent the treatment of CMS, FBS or serum starvation
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| Contributor(s) |
Li J, Zhang X |
| Citation missing |
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| Submission date |
Nov 29, 2021 |
| Last update date |
Dec 02, 2021 |
| Contact name |
Jiao Li |
| E-mail(s) |
jiaoli@zmu.edu.cn
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| Phone |
18785250841
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| Organization name |
Zunyi Medical University
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| Street address |
No.6 West Xuefu Road
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| City |
Zunyi |
| State/province |
Guizhou |
| ZIP/Postal code |
563006 |
| Country |
China |
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| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA784700 |
| SRA |
SRP348543 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE189845_KO_genes_fpkm_expression.txt.gz |
5.3 Mb |
(ftp)(http) |
TXT |
| GSE189845_WT_genes_fpkm_expression.txt.gz |
5.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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