|
| Status |
Public on Oct 30, 2009 |
| Title |
MM-038_miRNA |
| Sample type |
RNA |
| |
|
| Source name |
Multiple myeloma patient MM-038
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: multiple myeloma patient
sex: F
age at diagnosis (years): 67
stage (durie-salmon): IIA
monoclonal component: Gk
tc classification: TC2
related gene expression profiling (gep) data available (geo id): GSM341976
related genome-wide dna analysis data available (geo id): GSM403337
|
| 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).
|
| Label |
Cy3
|
| Label protocol |
Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) to the 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37°C for 30 min. The labeled RNA was purifed on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA).
|
| |
|
| Hybridization protocol |
Sample was hybridized on an Agilent microarray (G4470B) at 55°C for 17 hr in a rotating oven.
|
| Scan protocol |
Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 9.5 software (Agilent Technologies) was used to obtain the microarray raw data. The human miRNAs included in the platform were annotated according to Sanger miRBase Release 12.0.
|
| Description |
MicroRNA profiling data from multiple myeloma patient MM-038
|
| Data processing |
After discarding non-human miRNAs, the data were normalized using the Aroma Light package for Bioconductor. To overcome scaling biases due to background subtraction, the data were converted to obtain positive values throughout the dataset, at a minimum value of 1.
|
| |
|
| Submission date |
Aug 04, 2009 |
| Last update date |
Oct 30, 2009 |
| 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 |
GPL8227 |
| Series (1) |
| GSE17498 |
Identification of MicroRNA Expression Patterns and a MicroRNAs/mRNA Regulatory Network in Multiple Myeloma |
|
