Bladder epithelial cells with different degrees of malignancy: SV1 vs SV1 Cdcl2 vs T24

m5C-specific methylated small RNA immunoprecipitation microarray analysis in SV-HUC-1, Cd-SV-HUC-1 and T24 cells 1-5 μg of each total RNA sample was immunoprecipitated by 4 μg anti-5-methylcytosine antibody (Mab-006-500) with 1 mg DynabeadsTM M-280 Sheep Anti-Mouse IgG (Invitrogen, 11201D) in 500 μL RIP buffer. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were enzymatically labeled with Cy5 and Cy3 respectively in separate reactions using Arraystar’s standard protocols. The labeled RNAs were combined together and hybridized onto Arraystar Human small RNA Modification Microarray (8x15K, Arraystar) and the array was scanned in two-color channels by an Agilent Scanner G2505C.