|
| Status |
Public on Jan 31, 2019 |
| Title |
Total RNA from ground cells, Osteogenic medium, biological replicate 2_array |
| Sample type |
RNA |
| |
|
| Source name |
hBMSCs on ground cultured in osteogenic medium
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: bone marrow mesenchymal stem cells
location: ground
medium: osteogenic
|
| Growth protocol |
Standard Medium (SM): DMEM (Dulbecco’s Modified Eagle’s medium) supplemented with 12.5 mM HEPES, 10 U/mL heparin, 200 mM glutamine, 500 μg/mL streptomycin sulphate, 600 μg/mL penicillin.
Osteogenic Medium (OM): SM added with 0.1 M ascorbic acid, 10 mM b-glycerophosphate, and 10-8 M 1,25(OH)2D3 (Vit D3).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were preserved in RNAlater; resuspended by scraping in Trizol (Thermo Fisher Scientific) for total RNA extraction.
|
| Label |
biotin
|
| Label protocol |
5-30 ng of high quality total RNA were used to synthesize Biotin-labeled cDNA targets. Double stranded cDNA synthesis and related cRNA was performed with Nugen® Pico WTA Systems V2 (NuGEN Technologies, Inc). With the Encore® Biotin Module (NuGEN Technologies, Inc) was synthesized the fragmented and labeled cDNA.
|
| |
|
| Hybridization protocol |
Hybridization was performed onto Affymetrix Gene Human 1.0 ST arrays (28.869 genes) (Affymetrix, Santa Clara, CA,USA).
|
| Scan protocol |
GeneChip arrays were scanned using an AffymetrixGeneChip® Scanner3000 7G using default parameters. AffymetrixGeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files
|
| Description |
GM_OM_2
|
| Data processing |
Partek Genomics Suite v 6.4 was used for analysis of microarray data
The list of the differentially expressed genes was obtained using ANOVA. A 1.3-FC cutoff value coupled with p <0.05 and a false discovery rate (FDR) filter were used to distinguish statistically higher or lower gene expression from random variation
|
| |
|
| Submission date |
Jul 07, 2017 |
| Last update date |
Jan 31, 2019 |
| Contact name |
Silvia Bradamante |
| E-mail(s) |
[email protected]
|
| Phone |
+390264485030
|
| Organization name |
CNR-ISTM, Institute of Molecular Science and Technology
|
| Street address |
Via Golgi 19
|
| City |
Milan |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE100930 |
SCD – Stem Cell Differentiation on board the International Space Station [microarray on total RNA] |
| GSE100933 |
SCD – Stem Cell Differentiation on board the International Space Station: the problem of human bone loss |
|
