|
| Status |
Public on Aug 05, 2009 |
| Title |
1000 ng total RNA from vesicles |
| Sample type |
RNA |
| |
|
| Source name |
microvesicles (MV) derived from human liver stem cells (HLSC)
|
| Organism |
Homo sapiens |
| Characteristics |
total rna quantity: 1000 ng
cell type: microvesicles (MV) derived from human liver stem cells (HLSC)
|
| Growth protocol |
MV were obtained from supernatants of HLSC cultured overnight in α-MEM deprived of FCS. The viability of HLSC at the time of MV collection was >99% as detected by trypan blue exclusion. After centrifugation at 2,000 g for 20 minutes cell-free supernatants were centrifuged at 100,000 g (Beckman Coulter Optima L-90K ultracentrifuge) for 1 hour at 4°C, washed in serum-free medium 199 containing Hepes 25mM (Sigma) and submitted to a second ultracentrifugation in the same conditions (21,23). The protein content of MV preparation was quantified by Bradford method (Bio-Rad, Hercules, CA, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from MVs using TRIZOL reagent (Invitrogen) following the procedure suggested by the manufacturer. Total RNA was quantified spectrophotometrically (Nanodrop ND- 1000, Wilmington DE, USA).
|
| Label |
biotin
|
| Label protocol |
cRNA was synthesized using three different quantities of total RNA (0.25 μg, 0.5 μg and 1 μg). cRNA synthesis and labeling was done using Illumina RNA Amplification Kit (Ambion) following the procedure suggested by manufacturer.
|
| |
|
| Hybridization protocol |
Sentrix® Human- 6 Expression BeadChip hybridization, washing and staining were also done as suggested by the manufacturer.
|
| Scan protocol |
Arrays were scanned on Illumina BeadStation 500 (Illumina, San Diego, CA, USA).
|
| Description |
1000 ng total RNA from vesicles
|
| Data processing |
BeadChip array data quality control was performed using Illumina BeadStudio software version 3.0. Transcript average intensity signals were calculated with BeadStudio without background correction. Raw data were analyzed using Bioconductor. Average transcript intensities were log2 transformed and normalized by loess method.
|
| |
|
| Submission date |
Apr 06, 2009 |
| Last update date |
Aug 05, 2009 |
| Contact name |
Raffaele A Calogero |
| E-mail(s) |
raffaele.calogero@unito.it
|
| Phone |
++39 0116706454
|
| Organization name |
University of Torino
|
| Department |
Molecular Biotechnology Center
|
| Lab |
Bioinformatics and Genomics Unit
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
To |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6884 |
| Series (1) |
| GSE15569 |
Human liver stem cells-derived microvesicles accelerate hepatic regeneration in partially hepatectomized rats |
|
