To delete the SNP rs55958994-containing enhancer-like region, 22Rv1 cells were transfected with plasmids containing Cas9 and guide RNAs targeting the enhancer-like region. Colonies were derived from single cells and tested for the loss of the target region. Cell clones were genotyped, and three clones with homozygous deletion of the rs55958994-containing region and three control clones were used for RNA-seq analysis. The single-guide RNA (sgRNA) information is listed in table S1, which was designed by using web-based tools at https://zlab.bio/guide-design-resources. To generate site-directed mutation of SNP rs55958994, we transfected 22Rv1 PCa cells with plasmids containing Cas9, guide RNAs targeting the enhancer-like region, and DNA fragments containing (T) allele as repair templates. Double-nicking strategy was taken to reduce undesirable off-target mutagenesis. The sgRNA information is listed in table S4, which was designed by using web-based tools at https://zlab.bio/guide-design-resources. The region containing mutation was amplified using specific primers (table S4), and SNP genotyping was performed by Sanger sequencing–based method.

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