Figure 2

Relative quantification and transcriptional orientation of intronic lncRNAs differentially expressed in ccRCC. Expression of (A) ncC11orf49, (B) ncHDAC5, (C) ncRAB31 and (D) ncSRPK1 was evaluated in tumor and adjacent nontumor paired samples from clear cell RCC patients by qPCR. Tumor expression relative to paired nontumor in each patient sample is shown. lncRNA expression was normalized by HPRT1 gene expression. The statistical significance of the differential expression was evaluated by the t-test (p < 0.05). (E) For each gene, strand-specific reverse transcription (RT) followed by PCR shows the presence of intronic messages transcribed from the antisense (AS) and/or the sense (S) strands, in a pool of 10 ccRCC tissues, in a pool of 10 matched nontumors, or in the 786-O tumor and the RC-124 nontumor kidney cell lines. A control (C) for the absence of RNA self-annealing during reverse transcription and for the absence of genomic contamination was performed with an RT reaction step without primer (+ RT, - RT primer), followed by PCR with the pair of primers for the corresponding lncRNA.