Transcriptomes of SIX1 deficient and control Rhabdomyosarcoma cells

Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Genetic and shRNA-mediated inhibition of SIX1 expression in RMS cells induces myogenic differentiation and impedes RMS tumor growth. To elucidate the mechanism by which SIX1 loss activates a differentiation program, we performed RNAseq in two SIX1 knockdown SMS-CTR cell lines and one control SMS-CTR cell line to profile changes in transcriptome. Overall design: RNAseq was performed in Fusion-Negative Rhabdomyosarcoma cells (SMS-CTR). Two SIX1 knockdown SMS-CTR cell lines (SMS-CTR SIX1 KD5, SMS-CTR SIX1 KD6) and one control SMS-CTR cell line (SMS-CTR SCRAMBLE) were used. Four replicates of Scramble, three replicates of SIX1 KD5, and two replicates of SIX1 KD6 were used. Due to severe proliferative deficits, only two replicates of the SIX1 KD6 cell line were used.