Additional file 5: of Drosophila melanogaster retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations

Work flow for high throughput sequencing and small RNA analysis (SMACR). (A) Drosophila cells were individually depleted of Dcr2, CPSF73, Symplekin, and GFP (or LacZ). An additional fifth sample was untreated. The untreated and GFP samples represent controls. RNA was isolated from each sample and fractionated into RNAs > than 200 nts and RNAs < 200 nts. Each sample was depleted of appropriate rRNAs followed by library construction in triplicate. RNA-seq was performed at Washington University while smRNA-seq was performed at University of Missouri-St. Louis. (B) Adapters were trimmed from the raw reads followed by filtering out all small RNAs larger than 30 nts. Small RNAs were mapped using Bowtie and were then sorted by feature: miRNA, transposon, hairpin, or non-coding RNA. The normalized read count of each unique small RNA mapping to each feature was calculated together with 3’ and 5’ and size abundance. (PDF 293 kb)