Genespring software version 7

Total RNA was isolated using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) and was submitted to ProfileXpert core facility (Lyon, France) for microRNA profiling. The samples were hybridized on human v.3 miRNA Agilent array according to manufacturer instructions (Agilent protocol version 2.2), and microarray data analysis was carried out using Feature Extraction software version 10.7 (Agilent, Santa Clara, CA, USA).
For better cross-array comparison, raw data were normalized with the Genespring software version 7.3.1 (Agilent), using two LabelingSpikes-InSignal (DMR_285 and DMR_31a) as internal standard. The threshold of detection was calculated using the normalized signal intensity of negative controls ±3 standard deviation. Spots with signal intensities below this threshold are referred to as (absent) with an arbitrary value of 0.01*, and denoted ‘A’ in the Tables S1 and S2. Quality of processing was evaluated by generating a scatter plot of 11 positive controls. Statistical comparison and filtering were performed using Genespring software 7.3.1 (Agilent). The average signal is averaged between two replicates, and log2 fold change is calculated between ΔCK2β and Mock conditions. The mean and standard deviation of the mean are then calculated to aggregate different probes signal of the same miRNA.
Both mRNA and miRNA datasets are available under the accession number GSE102267.

CpG methylation microarray analyses were performed using genomic DNA isolated from primary tumors and paired adjacent nontumor tissues from nine BCa patients with different stages (T1, n = 5; T2, n = 1; T3, n = 1; and T4, n = 2). CpG methylation microarray analysis was conducted as described previously [22 ] using human 244 k CpG island microarrays containing 237,000 oligonucleotide probes covering 27,800 annotated CpG islands (Agilent Technologies, CA, USA) according to the manufacturer’s instructions. Raw methylation microarray data were submitted to Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) with accession number GSE171369.
Methylation microarray data were analyzed using the Agilent Feature Extraction software version 9.3.2.1 and a GeneSpring software version 7.3.1 (Agilent, CA, USA). To determine differentially methylated targets between primary tumor and paired adjacent nontumor tissue samples, statistical analysis was performed using a parametric analysis of variance test with Benjamini and Hochberg multiple testing correction (P < 0.01), followed by fold change analysis. Next, multiple-probe enriched genes were further selected as methylation candidate genes if their probes yielded a positive call for methylation in the bladder primary tumor compared to non-cancerous tissues with at least two probes.