Expression profile of HNF1A knockdown and overexpression in 22RV1 and LNCaP cells respectively

To determine genes regulated by HNF1A in 22Rv1, we performed siRNA mediated knockdown of HNF1A using pooled siHNF1A (L-008215-00-0005 5 nmol) and pooled siSCR purchased from Dharmacon. RNA was harvested 3 days after transfection and gene expression profiling was performed. Similarly to determine genes regulated by HNF1A in LNCaP, we performed retroviral transduction of LNCaP cells in duplicate for HNF1A and empty vector control expression. cDNA for HNF1A in RC211201 vector (origene) was subcloned into a murine stem cell virus (MSCV)-based retroviral vector with hygromycin selection marker (Addgene). After 3 days of transduction, cells were selected for four days in hygromycin and later on RNA was harvested for gene expression profiling. Overall design: RNA profiles were generated by deep sequencing using Illumina HiSeq.

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Shukla S, Cyrta J, Murphy DA, Walczak EG, Ran L, Agrawal P, Xie Y, Chen Y, Wang S, Zhan Y, Li D, Wong EWP, Sboner A, Beltran H, Mosquera JM, Sher J, Cao Z, Wongvipat J, Koche RP, Gopalan A, Zheng D, Rubin MA, Scher HI, Chi P, Chen Y