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| Status |
Public on Nov 13, 2019 |
| Title |
matrix vesicles 3 |
| Sample type |
RNA |
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| Source name |
matrix vesicles, replicate 1
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| Organism |
Mus musculus |
| Characteristics |
tissue: matrix vesicles
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| Treatment protocol |
MC3T3-E1 cells were grown at 3,000 cells/cm^2 in osteogenic meium with beta-glycerophosphate.
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| Extracted molecule |
total RNA |
| Extraction protocol |
When the osteoid-like nodules formed, cultures were treated with 500 units/mL collagenase at 37 Cº for 45 min under static conditions for 15 min with shaking. Samples were then centrifuged at 20,000 x g for 20min, and wupernatants were centrifuged at 100,000 x g for 60 min. THe resultant pellets were resuspended in 100 mM mannnitol in 10 mM HEPES, followed by centrifugation at 350,000 x g for 30 min. Matrix vesicle pellets were resuspended in PBS.
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| Label |
Cy3
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| Label protocol |
Probe labeling using 100 ng of total RNA wss performed using a miRNA Complete Labeling.
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| Hybridization protocol |
Hybridization was performed using Hyb kit and a SurePrint G3 mouse miRNA microarray rel.17 kit.
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| Scan protocol |
miRNA profiling was analyzed using an Agilent G2539A microarray scanner with the software Scan Control (version A.8.5.1). Dye channel, Green; Scan region, Agilend HD (61x21.6mm); R/G PMT gain, 100%; Scan resolution, 3 micro m; No XDR.
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| Description |
miRNA in matrix vesicles
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| Data processing |
Data was processed using Feature Extraction (version 10.10.1.1); Grit template, 035430_D_F_20121221; FE protocol, miRNA_1010_Sep10. Data was analyzed using an analysis software GeneSpring GX (version 12.5.0. Select Technology, 35230_v18.0.
Nomalization, "percentile Shift=90"; Baseline Options, "Do not perform baseline transformation"; Statistical Analysis, "Moderated t-test" "Benjamin Hochberg FDR" "p value<0.05"; Fold Change, "Cut Off =1.1"
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| Submission date |
Nov 12, 2019 |
| Last update date |
Nov 13, 2019 |
| Contact name |
Tomoko Minamizaki |
| E-mail(s) |
[email protected]
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| Organization name |
Hiroshima University
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| Street address |
1-2-3, Kasumi
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| City |
Hiroshima |
| State/province |
Hiroshima |
| ZIP/Postal code |
7348553 |
| Country |
Japan |
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| Platform ID |
GPL15547 |
| Series (1) |
| GSE140242 |
Comprehensive analysis of miRNAs in matrix vesicles |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM4157921_3_NC3_GeneView.txt.gz |
5.5 Kb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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