|
| Status |
Public on Jun 22, 2012 |
| Title |
MSC |
| Sample type |
RNA |
| |
|
| Source name |
Mesenchymal stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: none
cell type: Mesenchymal stem cell
|
| Treatment protocol |
Human bone marrow MSC were treated or not with IL-1β (25 ng/mL) for twenty four hours at 37 ºC in a humidified incubator with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from BM-MSC using the High Pure RNA Isolation kit (Roche) and was quantified by spectrometry (NanoDrop ND-1000, NanoDrop Technologies).
|
| Label |
Cy3
|
| Label protocol |
800 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent p/n 5188-5339) according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Based on the protocol for One-Color Microarray-Based Gene Expression Analysis Version 5.5 (Agilent p/n 5188-5977), 3μg of labeled cRNA was hybridized with Whole Human Genome Oligo Microarray Kit (Agilent p/n G4112F) containing 41,000+ unique human genes and transcripts.
|
| Scan protocol |
Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol and data extracted using Agilent Feature Extraction Software 9.5.1 (http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx).
|
| Description |
Mesenchymal stem cell
|
| Data processing |
Signal was standardized across arrays using quantile normalization. Differential gene expression was carried out using the fold change. Gene set analysis was carried out for the Gene Ontology terms using FatiScan
|
| |
|
| Submission date |
Nov 16, 2011 |
| Last update date |
Jun 22, 2012 |
| Contact name |
Francisco García García |
| E-mail(s) |
fgarcia@cipf.es
|
| Organization name |
CIPF
|
| Department |
Bionformatics & Biostatistics Unit
|
| Street address |
Eduardo Primo Yúfera, 3
|
| City |
Valencia |
| ZIP/Postal code |
46012 |
| Country |
Spain |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE33755 |
Effect of IL-1β on mesenchymal stem cells |
|
