|
| Status |
Public on Apr 01, 2011 |
| Title |
ABI_Human Dermal Blood Vascular Endothelial Cells Donor 2 |
| Sample type |
RNA |
| |
|
| Source name |
Neonatal human foreskin
|
| Organism |
Homo sapiens |
| Characteristics |
CD45-/CD34+ Human Blood Vascular Endothelial Cell (BVEC).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.
|
| Label |
Chemiluminescent Digoxigenin-UTP labeled cRNA
|
| Label protocol |
Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4363105) according to the manufacturer’s protocol.
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| |
|
| Hybridization protocol |
Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.
|
| Scan protocol |
Scan protocol Chemiluminescent Detection Kit (P/N 4339627, http://docs.appliedbiosystems.com/pebiodocs/04339627.pdf) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).
|
| Description |
NA
|
| Data processing |
Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.
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| |
|
| Submission date |
Dec 16, 2006 |
| Last update date |
Apr 01, 2011 |
| Contact name |
Jay Woo Shin |
| E-mail(s) |
[email protected]
|
| Organization name |
ETH Zurich
|
| Department |
Institute of Pharmaceutical Sciences
|
| Lab |
Michael Detmar
|
| Street address |
Wolfgang-Paulistrasse 10; HCI H394
|
| City |
Zurich |
| State/province |
Zurich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL2986 |
| Series (3) |
| GSE6549 |
Identification of the vascular lineage-specific transcriptome |
| GSE6550 |
Identification of the vascular lineage specific transcriptome using two platforms |
| GSE6560 |
Vascular lineage-specific transcriptome |
|
