Drosophila melanogaster late third instar larval ovary and gonadal fatbody polyA+ RNA-Seq profiling.

Here we perform transcriptional profiling of late third instar larval ovaries and gonadal fatbody from Drosophila melanogaster w1118 flies. We designed this experiment to investigate the effect of protease treatment on dissected ovaries. We profiled ovaries without protease treatment with some fatbody still attached, fatbody alone dissected from around the ovaries, ovaries cleaned of fatbody using a papain/collagenase cocktail, and ovaries dissociated using a papain/collagenase cocktail. We then constructed polyA+ libraries and performed 50 bp stranded single end RNA-Seq. For each sample type we pooled 10-30 ovaries and collected biological quadruplicates. Sample types include: ovaries with some remaining fatbody (OF), fatbody dissected from around ovaries (FO), ovaries cleaned of fatbody using a papain/collagenase cocktail (OCP), and ovaries dissociated using a papain/collagenase cocktail (ODP). Within a sample type, pools of ovaries were collected at the same time, and different replicates and treatments were collected on different days. Samples were stored at -80ºC until RNA extraction and library preparation. We extracted RNA and constructed libraries simultaneously for all samples in a 96 well plate.