|
| Status |
Public on May 22, 2011 |
| Title |
N-003_5 |
| Sample type |
RNA |
| |
|
| Source name |
Human normal donor N-003
|
| Organism |
Homo sapiens |
| Characteristics |
legend: TC classification = TC1, TC2, TC3, TC4, TC5 (Hideshima et al. Blood, 2004; Agnelli et al., J.Clin.Oncol., 2005); N: Normal donor sample; MGUS: Monoclonal Gammopathy of Undetermined Significance sample; PCL: Plasma Cell Leukemia sample.
cell type: purified plasma cells (PCs)
sample type: N
|
| Treatment protocol |
Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).
|
| Description |
Gene expression profiling data from human normal donor N-003
|
| Data processing |
The probe-level signals were converted to expression values using the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.
|
| |
|
| Submission date |
May 12, 2011 |
| Last update date |
May 22, 2011 |
| Contact name |
Luca Agnelli |
| E-mail(s) |
luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
|
| Phone |
+390223903581
|
| Organization name |
IRCCS Istituto Nazionale dei Tumori
|
| Department |
Department of Advanced Diagnostics
|
| Street address |
Venezian 1
|
| City |
MILAN |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE13591 |
Integrated genomics approach to detect allelic imbalances in multiple myeloma |
| GSE16122 |
A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma |
|
