|
| Status |
Public on Apr 29, 2009 |
| Title |
siRNA beta3 1 HB00E90 |
| Sample type |
RNA |
| |
|
| Source name |
Cell Cultures
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Myeloma plasma
cell line: silenced for beta3
|
| Treatment protocol |
The Myeloma plasma cells were purified from needle marrow and cultured to obtain established cell lines
|
| Growth protocol |
Myeloma plasma cells, purified from needle marrow aspirates by Ficoll-Hypaque gradient centrifugation and subsequently enriched by using anti-CD138 MoAb conjugated magnetic beads (Miltenyi Biotech, Bologna, Italy).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using the RNeasy Micro kit (QIAGEN) and treated with DNase I to eliminate possible genomic DNA contamination.
|
| Label |
Dig-UTP
|
| Label protocol |
Digoxigenin-UTP labeled cRNA was generated and linearly amplified from 1 ug of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 2.0. Amount (10–70 μg) and quality of the DIG-labeled cRNA was controlled by the NanoDrop® ND-1000 spectrophotometer
|
| |
|
| Hybridization protocol |
Ten μg of DIG-labeled cRNA was hybridized to the Applied Biosystems Human Genome Survey Microarray. The AB Human microarray contains 33,096 60-mer oligonucleotide probes representing 29,098 individual human genes
|
| Scan protocol |
Array hybridization, chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer
|
| Description |
myeloma bone resorbing cell lines silenced for beta3
|
| Data processing |
Only microarrays showing average normalized signal intensity above 5,000 and a median background below 600 were included in the study. Signal intensities were imported into Spotfire and Intergomics software (Spotfire Inc., Cambridge, MA, USA) where inter-array quantile normalization was performed in order to minimise the effect of external variables introduced into the data. Quality filtering of unreliable spots (S/N<3) was performed before normalization
|
| |
|
| Submission date |
Apr 28, 2009 |
| Last update date |
Apr 28, 2009 |
| Contact name |
gabriella rodolico |
| E-mail(s) |
rodgab@email.it
|
| Organization name |
Second University of Naples
|
| Street address |
Via Costantinopoli 16
|
| City |
Naples |
| ZIP/Postal code |
80138 |
| Country |
Italy |
| |
|
| Platform ID |
GPL3307 |
| Series (1) |
| GSE15867 |
Analysis of human myeloma cell lines expressing beta 3 integrin |
|
