In this study, biological triplicate s RNA- and m RNA-seq libraries were sequenced for both RNAi conditions. In this exercise we will identify what small RNAs are present in Drosophila Dmel-2 tissue culture cells treated with either RNAi against core cleavage complex component Symplekin or blank (control) RNAi (published data available in GEO at GSE82128). Because of the long processing time for the large original files - which contained 7-22 million reads each - we have downsampled the original input data to include only a subset of usable reads. The original published study can be found here. To that end, in addition to s RNA-seq, m RNA-seq experiments were performed to determine whether targets of differentially expressed si RNAs were also differentially expressed. The goal of this study was to determine how si RNA expression changes in flies treated with RNA interference ( RNAi) to knock down Symplekin, which is a component of the core cleaveage completx. The data used in this tutorial are from polyphosphatase-treated s RNA sequencing (s RNA-seq) experiments in Drosophila. In this tutorial, we will examine expression of the pi RNA subclass of s RNAs and their targets in Drosophila melanogaster. micro RNAs (mi RNAs), Piwi-interaction RNAs (pi RNAs), and endogenous short interferring RNAs (si RNAs) - exhibit unique characteristics, and their relative abundances in biological contexts can indicate whether they are active or not. Through interactions with protein cofactors, these tiny s RNAs typically function by perfectly or imperfectly basepairing with substrate RNA molecules, and then eliciting downstream effects such as translation inhibition or RNA degradation. Small, noncoding RNA (s RNA) molecules, typically 18-40nt in length, are key features of post-transcriptional regulatory mechanisms governing gene expression.
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