Gene expression data from human erythroleukemic cells in a time dependent manner after PMA treatment

The molecular regulation of megakaryocytic differentiation is poorly understood. Using a myelogenous leukemia cell line, K562, which can partly recapitulate the process in response to phorbol 12-myristate 13-acetate (PMA), we performed a microarray-based gene expression profiling using Illumina HumanRef-8 Expression Beadchip to identify genes that play significant roles in megakaryopoiesis. Time course microarray data were obtained at 8 time points. Illumina HumanRef-8 Expression Beadchip has ~over 24,000 transcripts a piece. Duplicate experiments were performed for each time point. Here, we reported raw data of two independent experiments. After microarray data analysis, selecting genes with significant detection p-value produced ~14,000 probes out of total 23,920 probes. Quantile normalization was carried out for each dataset at 8 time points using the average expression value. The K-means clustering method (k=12) was used to classify those probes according to characteristic temporal pattern. We selected transcription factors shown fold changes in a time dependent manner to examine genes related for megakaryopoiesis. Finally, we can suggest that FosB which belongs to the Fos family of AP1 transcription factors is related in megakaryopoiesis. The K562, a human chronic myeloid leukemia cell line, was obtained from the American Type Culture Collection and cultured in RPMI containing 10% heat-inactivated fetal bovine serum (Hyclone) 100 unit/ml penicillin and 100ug /ml streptomycin in a humidified 5% CO2 atmosphere at 37 degrees C. Differentiation toward megakaryocytic lineage was induced by growing the 3 × 105 K562 cells in a six-well plate in media containing 20 nM, PMA dissolved in dimethyl sulfoxide (DMSO) for 0, 0.5, 1, 3, 6, 12, 24, and 48 hour. Control cultures were treated similarly with the solvent DMSO. Total RNA was extracted from two independent experiments using a RNeasy Mini Extraction Kit (Qiagen, Hilden, Germany). Biotinylated cRNA was prepared from 550 ng total RNA per sample using the Illumina TotalPrepTM RNA Amplification Kit (Ambion, Austin, TX) and hybridized to the Illumina HumanRef-8 Expression Beadchip (Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.