GSE202578
Next Generation Sequencing-based Quantitative Analysis of female whole body transcriptomes from mock-infected control (sucrose fed) vs Pseudomonas entomophila (P.e)  orally infected flies
Purpose: The goal of this RNA-Seq is to analyze the whole-body transcriptomes from mock-infected bvs oral P.e. infected flies to identify differentially expressed genes Abstract from associated manuscript: When infected by intestinal pathogenic bacteria, animals initiate both local and systemic defence responses. These responses are required to reduce pathogen burden but also to alter host physiology and behaviour to promote infection tolerance, and they are mediated through alterations in host gene expression. Here, we have used transcriptome profiling to examine gene expression changes induced by enteric infection with the gram-negative bacteria Pseudomonas entomophila (P.e) in adult female Drosophila. We find that infection induces a strong upregulation of metabolic gene expression, including gut and fat body-enriched genes involved in lipid transport, lipolysis, and beta-oxidation, as well as glucose and amino acid metabolism genes. Furthermore, we find that the classic innate immune deficiency (Imd)/Relish/NF-KappaB pathway is not required for, and in some cases limits, these infection-mediated increase in metabolic gene expression. We also see that enteric infection with P.e. down regulates the expression of many transcription factors and cell-cell signaling molecules, particularly those previously shown to be involved in gut-to-brain and neuronal signaling. Moreover, as with the metabolic genes, these changes occurred largely independent of the Imd pathway. Together, our study identifies many metabolic, signaling and transcription factor gene expression changes that may contribute to organismal physiological and behavioural responses to enteric pathogen infection. Results: RNA Seq differential expression analysis identified a significant (p<0.05,> 1.5 fold expression) change in 2835transcripts, with 1602 transcripts showing reduced expression levels and 1233 transcripts with elevated expression levels. Overall design: For each condition (mock -infected vs P.e. infected) there were 6 independent biological samples, each consisting of total RNA extracted from 5 adult female flies. The sucrose fed condition is the control and the 6 samples are labelled W-Sucrose 1-6; the infected samples are labelled W-Pe 1-6.