PolyA+ expression profiling of tubulin Gal4 driven targeted DamID in Drosophila melanogaster adults and gonads

Targeted DamID (TaDa) measures gene expression using a DNA adenine methyltransferase (Dam) fused to RNA polymerase II (Dam Pol II) to methylate DNA as the genome is transcribed (Southall, Gold et al. 2013, PMID: 23792147). Here we use traditional Illumina RNA-Seq to determine if a cell’s expression profile is affected by Dam Pol II expression. Twenty-four hours prior to collection, we ubiquitously drove UAS Dam or UAS Dam Pol II using a tubulin (tub) GAL4 regulated by a temperature sensitive tub GAL80[ts] (McGuire et al. 2003, PMID: 14657498) in adult Drosophila melanogaster (taxon: 7227) whole males, whole females, testes, and ovaries. There were a total of 24 samples: 2 conditions (Dam or Dam Pol II), 4 tissues (whole female, whole male, testis, and ovary), and 3 biological replicates. Each sample contained a pool of individuals. We collected samples on different days, but extracted RNA and constructed RNA-Seq libraries at the same time in a 96 well plate. We used Dam expression as the control to look at transcriptional changes caused by Dam Pol II.