Downregulation of ARID1B, a tumor-suppressor in the WNT subgroup medulloblastoma, activates multiple oncogenic signaling pathways

About 85% of WNT subgroup medulloblastomas exhibit the loss of one copy of chromosome 6. Loss of function mutations were identified in the ARID1B gene located on chromosome 6 in WNT subgroup tumors suggesting tumor suppressor role for ARID1B in WNT medulloblastomas. The expression of ARID1B was downregulated in the medulloblastoma cell line Daoy using two independent shRNA sequences in a doxycycline-inducible lentiviral vector tet-pLKO-puro and the effect of its downregulation on the gene expression profile was studied by the RNA-seq analysis Overall design: The expression of ARID1B was downregulated in a doxycycline-inducible manner in Daoy medulloblastoma cell line using the lentiviral vector tet-pLKO-puro. Total RNA was prepared from doxycycline-treated cells expressing the ARID1B 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