gender: female age (yrs): 45 tissue: bone marrow (BM) disease state: acute myeloid leukemia (AML) subtype: AML-M1 abnormality: NK
Extracted molecule
total RNA
Extraction protocol
Blasts and mononuclear cells were purified by use of NycoPrep 1.077A (Axis-Shield, Oslo, Norway) according to the manufacturer’s manual. Total RNA was isolated from each sample using the miRNeasy Mini Kit (Qiagen), Trizol reagent (Invitrogen), or guanidinium thiocyanate followed by cesium chloride-gradient purification.
Label
Cy3
Label protocol
0.5ug total RNA per sample was reverse transcribed, amplified and labeled with Cy3 using the Agilent one-color amplification protocol (Agilent Quick-Amp Labeling Kit, One-color; One-Color Microarray-Based Gene Expression Analysis).
Hybridization protocol
The amplified cRNA samples were hybridized overnight and then washed based on the protocol of the Agilent Oligo Microarray (One-Color Microarray-Based Gene Expression Analysis V5.7, GE 8x15K, Gene Expression Hybridization Kit).
Scan protocol
Array slides were scanned on a GenePix 4000B scanner at 570 PMT and 100% Power standard setting according to the manufacturer’s instruction (Molecular Devices Corporation, Sunnyvale, CA, USA).
Data processing
Array slide images were then analyzed using Agilent Feature Extraction software (9.5.1.1) to obtain gene expression signals and array QC reports. Partek Genomics Suite (Partek Inc., St. Louis, MO, USA) were used for the data normalization. Briefly, background-adjustment, quantile normalization, and log2-transformation were used to normalize and treat gene expression intensities, and then median-centering genes for each array and median-centering each gene across all arrays were conducted.
