small RNA  profiling through high-throughput sequencing
Total RNA isolated from the control and RA-inoculated root tissues of Arabidopsis (triplicate for each) was used for library preparation using Illumina Truseq small RNA library preparation kit. Adaptors and low-quality reads were removed by using adapter removal and filter tool of UEA sRNA workbench version. Reads from all six libraries which mapped to plant t/rRNAs were discarded by using the filter tool of sRNA workbench and the remaining reads were used to identify conserved miRNAs based on sequence similarity with miRBase database and novel miRNAs by using Mireap_0.22b. For all the predicted novel miRNAs, potential precursor secondary structure was obtained through RNA/folding annotation tool Vienna RNA package. Target genes for known and novel miRNAs were predicted by using psRNATarget tool. For differential expression analysis of miRNAs, edgeR method was used. The genes preferentially and specifically expressed in various tissues/organs were identified.