mRNA profiling of JHDM2 knockdown Drosophila midguts post-infection with Ecc15. Drosophila melanogaster

We performed an mRNA-sequencing experiment using Drosophila midgut to find JHDM2-dependent signaling pathways in response to bacterial challenge and downstream target genes that are epigenetically regulated across genome. The sequenced reads from Illumina Hiseq2000 that passed quality filters were mapped to Drosophila genome (dm3) using Tophat and then quantitatively analyzed by Cufflinks at the gene level. By comparing Wild type and JHDM2 knock-down samples post-infection with Ecc15, we profiled JHDM2-dependent gene expression changes induced by Ecc15 infection. Overall design: mRNA expression profiles of JHDM2 knockdown Drosophila midgut and control Drosophila midgut at 4 and 16hr post-infection with Ecc15 were examined by Illumina Hiseq2000.