normalization data transformation protocol
The scanned image of the microarray was converted to fluorescence intensities for 45,101 probe sets by using GeneChip Operating Software (GCOS ver. 1.2, Affymetrix). CEL files were processed using Data Mining Tools(Affymetrix) and Microarray Suite version 5.0 (MAS 5.0) for background correction and probe summarization.We extracted 17419 probes which detected as present in all 4 samples from 45101 probes. The data were normalized with R version 3.0.2. In global normalization, the trimmed mean target intensity of each array was arbitrarily set to 500. The expression data was log2 transformed. ID_REF = VALUE = GCOS normalized ABS_CALL = DETECTION P-VALUE =
array scanning protocol
Images were scanned using an Affymetrix GeneChip Scanner 3000.
Mouse Genome 430 2.0 Array (Affymetrix Inc., Santa Clara, CA) was used for hybridization. The array was stained and washed with GeneChip Fluidics Station 450 (Affymetrix)
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
nucleic acid extraction protocol
Total RNA from 2 x 104 each fractionated leukemia cells based on NS-GFP level and c-Kit expression was isolated by using TRIzol (Invitrogen).