|
| Status |
Public on Sep 01, 2012 |
| Title |
Cyclopamin, 12h, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Coculture of 92% hMSCs and 8% huvEC, treated with cyclopamin, after 12 hours
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: co-culture of hMSC (92%) and hUVEC (8%)
treatment: Cyclopamine
|
| Treatment protocol |
coculture of 92% hMSCs and 8% huvEC (150,000 cells in total) in Deepwell 96 well-plates (adapted hanging-drop method) supplemented or not in cyclopamine, for 12 days. Medium was changed every third day by transferring the spherical aggregate to a new plate.
|
| Growth protocol |
Co-culture of hMSC (92%) and hUVEC (8%) were obtained by resuspending a total of 150,000 cell per spherical aggregate in 2 ml of differentiation medium and then seeded in a well of a Deepwell 96 well-plate (Nunc).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by using an RNeasy mini kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix GeneArray Scanner3000
|
| Description |
The effect of Cyclopamine on expression of Hedgehog, angiogenesis and axon guidance marker genes was analyzed by seeding a coculture of 92% hMSCs and 8% huvEC (150,000 cells in total) in Deepwell 96 well-plates (adapted hanging-drop method) supplemented or not in cyclopamine, for 12 days.
|
| Data processing |
The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. Gene expression profiling was performed using arrays of HG133 Plus2 -type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.
|
| |
|
| Submission date |
Jun 10, 2010 |
| Last update date |
Sep 01, 2012 |
| Contact name |
Carsten Sticht |
| Organization name |
University Heidelberg
|
| Department |
ZMF
|
| Street address |
Theodor-Kutzer-Ufer
|
| City |
Mannheim |
| ZIP/Postal code |
68169 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10526 |
| Series (1) |
| GSE22293 |
Engineering endochondral ossification using Sonic Hedgehog for bone regeneration |
|
