Whole Genome Microarray Analysis of BMSCs

Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Hilden, Germany) and assessed using Nano Drop 2000 (Thermo Scientific, Wilmington, DE). Microarray expression experiments were performed on 4 × 44 K Whole Human Genome Microarray (Agilent technologies, Santa Clara, CA, USA) according to our protocols [24 (link)]. Generally, 0.5 µg of BMSC RNA was labeled with Cyanine 5-CTP and Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) was labeled with Cyanine 3-CTP using a Quick Amp Labeling kit (Agilent). After purification, 825 ng of labeled cRNA from BMSC and reference RNA was pooled, fragmented and then hybridized on 4 × 44 K microarrays for 17 h at 65 °C. Images of the arrays were acquired using a microarray scanner G2505B (Agilent technologies) and image analysis was performed using feature extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied using default settings.