For samples 1-24: Samples were crosslinked in formaldehyde and lysed, followed by sonication. For samples 25-32: OSCs were resuspended in Trizol, flies homogenized in Trizol. RNA was isolated using RNeasy mini prep column (Qiagen). For samples 33-36: Flies were homogenized in Trizol and RNA extracted using Phenol/Chloroform For samples 1-24: NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® For samples 25-32: NEBNext Poly(A) mRNA magnetic Isolation Module (NEB), followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB) For samples 33-36: Adapted from: Jayaprakash, Anitha D. et al. “Identification and Remediation of Biases in the Activity of RNA Ligases in Small-RNA Deep Sequencing.” Nucleic Acids Research 39.21 (2011): e141. PMC. Web. 22 Oct. 2018.