Total RNA quality and quantity were analyzed with an Agilent 2100 Bioanalyzer (Agilent Technologies) and a NanoDrop 1000 ultraviolet-visible spectrophotometer (Thermo Fisher Scientific). Microarray experiments were performed at single-color hybridization. Total RNA was amplified and labeled with the low-input Quick-Amp Labeling Kit (Agilent Technologies). Brief, mRNA was reverse-transcribed and amplified with an oligo-dT-T7 promoter primer and labeled with cyanine 3-CTP. After precipitation, purification, and quantification, 1.25 μg of each labeled complementary RNA was fragmented and hybridized to whole-genome mouse 4X44K multipack microarrays (Agilent-014868, whole mouse genome 4X44K microarray kit, Agilent Technologies) according to the manufacturer’s protocol. Scanning of the microarrays was performed with 5-μm resolution with a G2565CA high-resolution laser microarray scanner (Agilent Technologies) with extended dynamic range. Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted MAGE-ML files were analyzed further with the Rosetta Resolver Biosoftware, Build 7.2.2 SP1.31 (Rosetta Biosoftware), and the extracted .txt files were further analyzed with R scripts and the associated BioConductor limma package (84).

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