|
| Status |
Public on Jun 25, 2013 |
| Title |
Plasma cell leukemia PCL-005_Gene1.0_2 |
| Sample type |
RNA |
| |
|
| Source name |
Human bone marrow plasma cells from primary plasma cell leukemia patient PCL-005
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human bone marrow plasma cells
disease state: primary plasma cell leukemia
genetic variation: del(13) -; del(17p)-; 1q gain+; HD+; t(11;14)+
|
| 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 |
5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).
|
| |
|
| Hybridization protocol |
The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol.
|
| Scan protocol |
Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).
|
| Description |
Gene expression profiling data from human primary plasma cell leukemia patient PCL-005
|
| Data processing |
The raw intensity expression values were processed by Robust Multi-array Average (RMA) complete procedure with the re-mapped Chip Definition Files (CDF) from BrainArray libraries version 15.0.0 available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.asp.
|
| |
|
| Submission date |
Jul 26, 2012 |
| Last update date |
Jun 26, 2013 |
| Contact name |
Luca Agnelli |
| E-mail(s) |
[email protected], [email protected]
|
| 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 |
GPL16522 |
| Series (1) |
| GSE39683 |
Small nucleolar RNAs and small Cajal body-specific RNAs show distinct transcriptional profiles in the context of the molecular heterogeneity of multiple myeloma. |
|
