Project description:To understand the effects of the microbiome of Drosophila melanogaster on host gene expression, we compared the transcriptome of guts from conventionally reared flies to their axenically (germ-free)-reared counterparts. Our analysis used dissected intestines from 4-7 day-old adult females and included two wild-type fly lines, OregonR and CantonS, as well as an immune-deficient line, RelishE20. With one of the wild-type lines, CantonS, we also looked at the impact of microbiome on the transcriptional profile of dissected intestines from aged cohorts (35-40 day-old females) and young (4-7 day-old) non-gut tissues (all tissues remaining from samples dissected for the analysis of guts.
Project description:Male flies were crossed to virgins of genotype yw;esg-Gal4,UAS-GFP;tub-Gal80ts/Tm3,Sb. Progeny was collected and aged 3-4 days before shifting for 7 days to 29 degrees to induce RNAi expression. Guts were dissected for 2 biological replicates/condition, each containing 80-100 guts, dissociated and GFP-positive cells were FACS-sorted. RNA was isolated using the PicoPure RNA-isolation kit and libraries were generated. Sequencing was done by distributing the 4 libraries over 5 lanes on the Illumina HiSeq2000 platform.
Project description:Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. Identifying these groups of co-expressed genes is important to the functional annotation of genomes and understanding the evolutionary fates of the clustered genes. We used microarrays to measure gene expression in seven closely related Drosophila species, to identify domains clusters within a species of Drosophila (D. simulans) and that are evolving among species in the D. melanogater subgroup. Experiment Overall Design: Assays were carried out on three independent (biological) replicates per species for a single line of the following five species: D.yakuba (Tuscon Stock Center Number: 14021-0261.00), D.santomea (TSCN: 14021-0271.00), D.teissieri (TSCN: 14021-0257.00), D.mauritiana (David 105, TSCN: 14021-0241.01), D.sechellia (Roberstson, TSCN: 14021-0248.21). Three biological replicates for D.melanogaster. The samples assayed for D.melanogaster reflect an even genotypic contribution of 10 isogenic lines developed from a wild population (Winters, CA) and crossed in a round-robin design.For D. simulans, three replicate arrays were used to assay each of 10 round-robin crosses between 10 isogenic lines developed from the same population. the entire data set therefore included a total of 48 independent transcript assays covering seven Drosophila species in the D.melanogaster subgroup
