SMARCA4 knockdown upregulates expression of myogenic genes in medulloblastoma

SMARCA4 gene is mutated in a subset of Group 3 medulloblastomas. ShRNA mediated downregulation of SMARCA4 expression in three Group 3 medulloblastoma cell lines upregulated the expression of myogenic/muscle differentiation related genes as studied by the transcriptome analysis. The expression of SMARCA4 was downregulated in a doxycycline-inducible manner in Group 3 medulloblastoma cell lines using the lentiviral vector tet-pLKO-puro. Total RNA was prepared from doxycycline-treated cells expressing the SMARCA4 shRNA and those expressing the vector alone and the parental cells . Libraries were prepared from the polyA-enriched RNA fraction using the Illumina Truseq RNA library preparation kit and sequenced on the Illumina Hiseq 2500 platform