FGFRs regulate PCa development and progression, but the role of the recently found FGFR-like 1 (FGFRL1) remains unclear. The data consists of gene expression profiles of mouse subcutanous xenograft tumors generated of human PC3M prostate cancer cells with stable knockdown of FGFRL1 gene and of the control xenografts. Overall design: Control PC3M cells with scrambled sh-RNA tarnsfection or with FGFRL1 knock-down by sh-RNA were inoculated subcutaneously to athymic nu/nu mice. Tumors wer harvested at day 45. The RNAseq samples include RNAs from five control tumors (derived from ctrl-sh8 cells) and five tumors with FGFRL1 knockdown (derived from FGFRL1-sh11 cells).