Robust manipulation of the behavior of Drosophila melanogaster by a fungal pathogen in the laboratory eLife, 2018 Jul 26

"( A ) Proportion of reads aligned to D. melanogaster reference (mRNA) versus E. muscae 'Berkeley' references (de novo transcriptome and de novo annotated mRNAs in genome) using bowtie2. Samples are separated into controls (healthy animals who were mock exposed), exposed (animals who exposed to E. muscae 'Berkeley' and were alive at the time of sampling) and cadavers (animals who were killed by E. muscae 'Berkeley', dead at the time of sampling) and are color-coded according to the time point at which they were collected (i.e. 24, 48, 72, 96 or 120 hr). ( B ) E. muscae 'Berkeley' expression data from E. muscae 'Berkeley'- exposed and cadaver samples calculated from alignment to de novo E. muscae transcriptome. Complete linkage hierarchical clustering by gene was performed in Gene Cluster 3.0 after filtering out genes that are not expressed at least at ten TPM in at least three out of 42 samples (9500 transcripts total), then log transforming and centering on the mean value for each transcript. Samples are ordered by percentage of E. muscae 'Berkeley' reads as a fraction of the total reads aligned (above). The scale bar for the heatmap is given to the right of the plot. ( C ) E. muscae 'Berkeley' expression data from E. muscae 'Berkeley'-exposed and cadaver samples calculated from alignment to de novo E. muscae genome. Complete linkage hierarchical clustering by gene was performed in Gene Cluster 3.0 after filtering out genes that are not expressed at least at two TPM in at least three out of 42 samples (3104 transcripts total), then log transforming and centering on the mean value for each transcript. Samples are ordered by percentage of E. muscae 'Berkeley' reads as a fraction of the total reads aligned (above). The scale bar for the heatmap is given to the right of the plot. ( D ) D. melanogaster expression data from control, E. muscae 'Berkeley'- exposed and E. muscae 'Berkeley'-killed cadavers. Complete linkage hierarchical clustering by gene was performed in Gene Cluster 3.0 after filtering out genes that are not expressed at least at two TPM in at least three out of 42 samples (10,746 transcripts total), then log transforming and centering on the mean value for each transcript. Samples are ordered by percentage of E. muscae 'Berkeley' reads as a fraction of the total reads aligned (above). The scale bar for the heatmap is given to the right of the plot. <t>Heatmaps</t> are scaled identically between panels ( B-D ). "