|
| Status |
Public on Jan 01, 2012 |
| Title |
EMPs |
| Sample type |
RNA |
| |
|
| Source name |
human ESC derived mesenchymal progenitors
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: embryonic mesenchymal progenitors
|
| Treatment protocol |
Stem cells were cultured in undifferentiated conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol® Reagent (Gibco-Invitrogen, USA), and followed by processing with the RNeasy Mini Kit (Qiagen, Germany). The extracted RNA was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA), with purity assessed by using a Bioanalyzer 2100 (Agilent Technology, USA) using the RNA 6000 nano labchip kit (Agilent Technologies, USA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) in accordance with the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes. Correspondingly fragmented labeled cRNA was then hybridized to the custom stem cell 8 x 15K oligo microarray (Agilent Technologies, USA) at 60°C for 17 hours.
|
| Scan protocol |
After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.
|
| Description |
Gene expression profiling
|
| Data processing |
The scanned images were analyzed by Feature extraction 9.5.3 software (Agilent Technologies, USA), an image analysis and normalization software for quantification of signal and background intensity. Normalized signal was generated from gProcessedSignal after normalization by 75th percentile. Data was generated by subtracting the mean background light intensity from the mean signal intensity then corrected for multiplicative surface.
|
| |
|
| Submission date |
Oct 13, 2009 |
| Last update date |
Jan 01, 2012 |
| Contact name |
Men-Luh Yen |
| Organization name |
National Taiwan University
|
| Street address |
No.1, Sect. 1, Jen-Ai Road
|
| City |
Taipei |
| ZIP/Postal code |
100 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL9443 |
| Series (1) |
| GSE18543 |
Mesenchymal progenitors from hESCs & profiling vs. BMMSCs |
|
