RNA-seq and ChIP-seq assays were performed in triplicate and for each biological replicate we dissected ovaries from approximately 30 female flies (2-4 days old). Total RNA was extracted using Trizol reagents (Life Technologies) and treated with turbo DNase-free kit (Ambion) to eliminate traces. of genomic DNA. DNA-free total RNA was subjected to two rounds of rRNA depletion using the Ribo-Zero rRNA removal kit (Epicentre) as per the manufacturer's instructions. The same ChIP protocol was employed for the ChIP-seq assays as previously described (Pane et al. 2011; Blythe et al. 2009). The Cuff-EGFP expressing transgenic line, GFP antibodies and the conditions used for the Cuff ChIP-seq experiment were previously described (Pane et al. 2011; Blythe et al. 2009). The RNA-seq library preparation was obtained with the ScriptSeq v2 kit (Epicentre) and the libraries were sequenced on the Illumina platforms. Chromatin fragments were used to generate DNA libraries with the ChIP-seq DNA Sample Prep kit (Illumina).
GEO Accession
GSM2604558