|
| Status |
Public on Oct 01, 2013 |
| Title |
CMLbonemarrow_variant 3 |
| Sample type |
RNA |
| |
|
| Source name |
CML_bone marrow_variant
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
disease type: chronic myeloid leukemia (CML)
translocation type: variant t(9;22) rearrangement
tissue: bone marrow
cell type: total white blood cells
|
| Treatment protocol |
Total white blood cells were isolated from CML BM samples by hypotonic red cell lysis, washed, transferred into a guanidinium isothiocyanate-containing buffer, and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole RNA was extracted by ultracentrifugation in caesium chloride density gradient. RNA quality was determined using the 2100 Bioanalyzer; only cellular samples of high quality characterized by RNA integrity numbers ranging from 8 to 10 were selected.
|
| Label |
Cy3
|
| Label protocol |
Twenty-five nanograms of each sample were labeled using the Low Input Quick Amp Labeling kit (Agilent).
|
| |
|
| Hybridization protocol |
Labeled cRNAs were hybridized for 17 hours at 65°C and 10 RPM on the Agilent SurePrint G3 Human GE 8x60K Microarray slide (Agilent Technologies) using the Agilent’s Microarray Hybridization Oven.
|
| Scan protocol |
Slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies) according to the Agilent_G3_GX_1Color protocol.
|
| Description |
SAMPLE 3
|
| Data processing |
Scanned images were processed using the Agilent Feature Extraction software (v10.7.3.1), raw data were quantile normalized and differentially expressed genes were selected by unpaired t-test and Multiple Testing Correction of Benjamini-Hochberg, considering as statistically significant those presenting a p-value less than 0.05 and a fold-change equal or higher than 2.
|
| |
|
| Submission date |
Oct 05, 2012 |
| Last update date |
Oct 01, 2013 |
| Contact name |
Francesco Albano |
| E-mail(s) |
francesco.albano@uniba.it
|
| Organization name |
University of Bari
|
| Department |
D.E.T.O.
|
| Lab |
Hematology Section
|
| Street address |
P.zza G. Cesare, 11
|
| City |
Bari |
| ZIP/Postal code |
70124 |
| Country |
Italy |
| |
|
| Platform ID |
GPL14550 |
| Series (1) |
| GSE41375 |
Gene expression profiling of chronic myeloid leukemia with variant t(9;22) reveals a different signature from cases with classic translocation. |
|
