|
| Status |
Public on Feb 10, 2017 |
| Title |
mirMM.069-MM95db |
| Sample type |
RNA |
| |
|
| Source name |
Newly-diagnosed MM patient 069
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: multiple myeloma
tissue: primary tumor
t(4;14) translocation: 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).
|
| Label |
biotin
|
| Label protocol |
500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol.
|
| |
|
| Hybridization protocol |
Byotin-labeled RNA samples were hybridized for 16 hours at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Scanning of the arrays was performed using the GeneChip Scanner 7G.
|
| Description |
microRNA expression data from multiple myeloma newly-diagnosed primary tumor.
|
| Data processing |
Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 18 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/version.html). Annotations were then updated to miRBase Release 20 definition using the mirna.diff files available at the miRbase website
|
| |
|
| Submission date |
Oct 11, 2016 |
| Last update date |
Jul 13, 2018 |
| 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 |
GPL16384 |
| Series (2) |
| GSE87828 |
In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (95 MM miRNA data sets) |
| GSE87830 |
In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma |
|
| Relations |
| Alternative to |
GSM1721935 |
| Reanalyzed by |
GSM3271451 |
