(A): Methylation specific PCR of CASP8, MASPIN, TMS1 and MDR1 in prostate cancer cells. DNA from prostate cancer cells were Bisulfite modified using EZ methylation kit (Zymo Research) and then PCR done using methylation specific primers and unmethylation specific primers. Because in the cells sometimes methylated and unmethylated both copies are present, so depending upon the number copies they get amplified. (B): Methylation specific PCR of CASP8, MASPIN, TMS1 and MDR1 in 5-aza-dC (5μM/48hrs) treated prostate cancer cells. (C) Bisulfite sequencing chromatogram of TMS1 gene showing methylation in LNCaP, DU145 and PC3, partial methylation in PC3 and Unmethylation in RWPE1. (B): Diagrammatic representation of methylation pattern of TMS1 and MDR1 gene at different promoter positions in RWPE1, LNCaP, DU145 and PC3. Dark circles (●) represents methylated sites, shadowed circles (An external file that holds a picture, illustration, etc.Object name is nihms159165ig1.jpg) represent partially methylated sites and blank circles (○) represents unmethylated sites in TMS1 and MDR1 promoter region.
(Mishra DK, Chen Z, Wu Y, Sarkissyan M, Koeffler HP, Vadgama JV. Global methylation pattern of genes in androgen-sensitive and androgen-independent prostate cancer cells. Mol Cancer Ther. 2010 Jan;9(1):33-45.)
亚硫酸氢盐处理后测序法（bisulfite sequencing PCR BSP）
Rad23b and Ddit3 methylation determined by BSP. Bisulfite treated DNA was amplified by PCR with BSP primers. PCR products were cloned into the pUC57 vector, and five clones selected and sequenced from each sample. Methylation level was defined as the ratio of methylated CpG sites in all clones. (A) Typical sequencing results; (B) early effects, tissues were collected 2 h postirradiation; (C) delay effects, 1 month postirradiation. *P,0.05 versus control.
Wang J, Zhang Y, Xu K, Mao X, Xue L, Liu X, Yu H, Chen L, Chu X. Genome-wide screen of DNA methylation changes induced by low dose X-ray radiation in mice. PLoS One. 2014 Mar 10;9(3):e90804.）
RIP（RNA Binding Protein Immunoprecipitation）RNA结合蛋白免疫沉淀
图. MS2- RIP实验原理图（表达Lnc-A的质粒富集miRNA1miRNA2的效率比不表达Lnc-A的MS2组明显提高。通过对照，说明MS2-A可以与miRNA1和miRNA2相互结合）
RNA pull down
图. pull down下来的蛋白银染图。根据胶上条带的差异情况和实验目的，选择质谱或者WB鉴定pull down下来的蛋白
（C Cao, Zhang T, Zhang D, et al.The long non-coding RNA, SNHG6-003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma. Oncogene. 2017 Feb 23;36(8):1112-1122. ）