title: GSM5549988: Input sample of Udd ChIP-seq from udd/+ ovaries; Drosophila melanogaster; ChIP-Seq
library_construction_protocol: RNA-seq: Total RNA samples were isolated from ovaries using Trizol reagent (Invitrogen) according to the standard protocol and treated with DNase using the DNA-free DNA Removal Kit (Invitrogen). rRNA was removed by hybridization of 200 ng of total RNA with biotinylated oligonucleotides complementary to different regions of rRNA followed by binding to Dynabead MyOn Streptavidin C1 (Invitrogen). After precipitation, supernatants containing rRNA-depleted RNA were precipitated with isopropanol and used for libraries preparation. ChIP-seq: ChIP using guinea pig anti-Udd (a gift from Michael Buszczak) was performed according to the published procedure (Chanas et al., 2004). Chromatin was fragmented by sonication on Vibra-Cell (Sonics) with amplitude 15% during 35 pulses of 10s with 10s pause intervals. RNA Library Prep Set V3.1 for RNA-seq Accel-NGS 1S Plus DNA Library Kit for ChIP-seq ChIP-seq; RNA-seq