|
| Status |
Public on Oct 12, 2012 |
| Title |
Primary Plasma Cell Leukemia PCL-020 Expression |
| Sample type |
RNA |
| |
|
| Source name |
Primary Plasma Cell Leukemia PCL-020
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: plasma cell
disease state: plasma cell leukemia
genome variation: translocation none
|
| 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 |
main IgH chromosomal translocations t(11;14), t(4;14), t(14;16), t(14;20)
Gene expression profiling data from human multiple myeloma patient PCL-020
|
| Data processing |
Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 31 and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions were summarized as median value for each sample.
|
| |
|
| Submission date |
Jul 16, 2012 |
| Last update date |
Oct 13, 2012 |
| 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 |
GPL6244 |
| Series (2) |
| GSE39381 |
Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations (Expression) |
| GSE39383 |
Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations |
|
