TEX cells were maintained in IMDM, 15% FBS, 2 mM L-glutamine, 1% Pen/Strep, 20 ng/mL SCF, 2 ng/mL IL3. M9-ENL1 cells were maintained in MEM, 20% FBS, 5% human adult plasma, 2mM L-glutamine, 1% Pen/Strep, 100 ng/mL SCF, 10 ng/mL IL3, 5 ng/mL IL7, 5 ng/mL FLT3-ligand.
Extracted molecule
total RNA
Extraction protocol
TriZol extraction of total RNA was performed according to the manufacturer's instructions.
Label
Biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol
The cDNA was fragmented, labeled and hybridized to Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA)
Scan protocol
standard Affymetrix protocol
Data processing
The data was processed using Bioconductor (affy package 1.30.0) by reading CEL files with default 'ReadAffy()' function. Data was background corrected with RMA, normalized by quantiles method, PM only correction, and then median polished. To account for batch variation, the log2 values were adjusted using ComBat (version 2) in GenePattern with a parametric Empirical Bayes priors distribution estimation method and without covariate analysis.
