Gene expression changes induced by SFRP2 silencing in RB383 retinoblastoma cells

To gain insight into signaling downstream of SFRP2 in retinoblastoma, we used siRNA to silence SFRP2 in RB383 retinoblastoma cells and assessed the resulting gene expression changes at 24 hours and 48 hours after siRNA transfection. RB383 cells were were transfected with either scrambled-siRNA or SFRP2-siRNA (Dharmacon) for 24 and 48 hours. Transfection was carried out using Lipofectamine™ RNAiMAX Transfection Reagent (Thermo Fisher) according to the manufacturer’s protocol. After 24 and 48 hours, cells were harvested and total RNA was extracted using TRIzol reagent (Invitrogen). For whole-genome transcriptome profiling, four libraries were generated from total RNA using a TruSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol (Illumina Inc.). Samples were sequenced on the Illumina HiSeq 3000 platform (Illumina Inc.) using the 51 base-pair single-read (50SR) sequencing module.