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| Status |
Public on Jul 07, 2020 |
| Title |
MSC_OPLL patient 2_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow-derived MSCs from OPLL patient (2)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: mesenchymal stem cells
disease state: ossification of the posterior longitudinal ligament (OPLL)
tissue: bone marrow
gender: female
|
| Treatment protocol |
To induce osteogenic differentiation, MSCs were cultured for 10 days in osteogenic differentiation medium containing DMEM with 10% FBS, 100 IU/ml penicillin, 100 IU/ml streptomycin, 0.1 μM dexamethasone, 10 mM β-glycerol phosphate and 50 μM ascorbic acid. All cells were cultured in 5% CO2 at 37 °C, and the culture medium was changed every 3 days.
|
| Growth protocol |
MSCs were isolated from bone marrow and cultured in DMEM medium containing 10% fetal bovine serum.All cells were cultured in 5% CO2 at 37 °C, and the culture medium was changed every 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA containing small RNA was extracted from MSCs by using the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.
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| |
|
| Hybridization protocol |
Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).
|
| Scan protocol |
The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent).
|
| Description |
Gene expression after culture in osteogenic differentiation medium for 10 days.
s2
|
| Data processing |
The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).
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| |
|
| Submission date |
Jul 06, 2020 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Zhaopeng Cai |
| Organization name |
Sun Yat-sen University
|
| Street address |
No. 3025, Shennan Middle Road, Futian District
|
| City |
Shenzhen |
| ZIP/Postal code |
518033 |
| Country |
China |
| |
|
| Platform ID |
GPL20115 |
| Series (1) |
| GSE153829 |
Aberrantly expressed lncRNAs and mRNAs of osteogenically differentiated mesenchymal stem cells in ossification of the posterior longitudinal ligament |
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