Supplementary Tables for "WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data". Supplementary Table 1. Statistics of GFT files obtained for human and mouse genome. The file reports the data of the filtering process and the final GTF data. Supplementary Table 2. Spike-in quantification. For each sample are shown the percentage of each piRNA-like molecules, respect to the raw reads count, using three quantification methods. Supplementary Table 3. Statistics of sncRNA data analysis for mouse cardiomyocytes. The file reports the results obtained using the two methods applied in the workflow and the list of top 100 expressed piRNAs. Supplementary Table 4. Differentially Expressed molecules found for GSE68246 dataset. In yellow are highlighted miRNA DE in common with Boo et al., in red and green are highlighted the up- and down-expressed molecules respectively, in light blue the molecules with an adjusted p-value less than 0.05. Supplementary Table 5. Differentially Expressed molecules found for BRCA TCGA dataset. In red and green are highlighted the up- and down-expressed molecules respectively, in light blue the molecules with an adjusted p-value less than 0.05. For DE piRNA molecules, the predicted possible target RNAs are also provided.