Figure 1: SNHG5 is deregulated in CRC.

(a) The expression levels of SNHG5 were profiled in clinical specimens by RNA-seq, where the RNA was extracted from tumour (C) or adjacent normal tissues (N) (****P value<0.0001, Mann–Whitney t-test). (b) Box plot representing stratified SNHG5 expression in CRC clinical specimens (N=normal adjacent tissue, A=adenomas, I–IV=CRC progression stages). The bottom line of each box represents the 1st quartile of sample population, the top line of the box represents the third quartile, while the middle quartile represents the population median. (***P value<0.001, ****P value<0.0001, Mann–Whitney t-test). (c) Schematic representation of the SNHG5 locus. (d) RNA-FISH of SNHG5 in red (Cy3) with a nuclear DAPI stain (blue) in HCT116 and TIG-3 cells. Scale bar, 50 μm. (e) RNA from the nuclear (N) and cytosolic (C) fractions were isolated from HCT116 and TIG-3 cells and SNHG5 levels measured using qRT–PCR. U50A and ACTB were used as nuclear and cytosolic controls, respectively. The expression values for each transcript are relative the total RNA input and normalized on the nuclear fraction expression levels. Error bars represent s.e. from one representative experiment. (f) qRT–PCR. HCT116 cells were transfected with 50 nM siSNHG5-1-2 or control siRNA and the RNA collected after 36 h. SNHG5 expression data are showed normalized to the GAPDH housekeeping gene and normalized to the non-targeting control siRNA. (g) Venn diagram representing the number of genes altered in HCT116 cells following siSNHG5-1-2 transfection after 36 h (log2 fold change> ±3, FDR<0.05). (h) Gene ontology annotation. Statistical overrepresentation test (Bonferroni-corrected) was applied to identify gene categories affected by SNHG5 depletion.