Protective microbes alter the transcriptional response of Caenorhabditis elegans nematodes to pathogenic infection

We sequenced the transcriptome of a host (Caenorhabditis elegans) following its interaction with a non-native bacterium (Enterococcus faecalis) that has protective traits against the pathogen, Staphylococcus aureus. We also investigated the impact that the evolutionary history of the protective bacterium has on the transcriptional history of the host. We tested protective bacteria that had either coevolved against the pathogen within C. elegans, or had evolved on its own within C. elegans. We generated the data over two independent experiments, "1" and "2". Within each independent experiment we included all the comparisons and controls required for each question, i.e. no comparisons were made across the independent experiments. In experiment 1, we measured the transcriptional response to three E. faecalis treatments and a control treatment of Escherichia coli OP50, which is widely used as a food source for C. elegans. We included 5 independent biological replicates for each of these treatments. In experiment 2, we measured the transcriptional response to these same three E. faecalis treatments in the presence of S. aureus, along with a treatment where C. elegans were exposed to just S. aureus alone. We also included the control treatment of Escherichia coli OP50. We included 5 independent biological replicates for each of these treatments. Results and the full materials and methods for experiment 1 are included in one manuscript (insert bioRxiv link here when uploaded), and results ad full materials and methods for experiment 2 are included across two manuscripts, (BioRxiv https://doi.org/10.1101/857540 and insert bioRxiv link here when uploaded). All samples were sequenced evenly across 5 units of a flow cell and were delivered in two batches. The first 3 units were delivered together and the 2 remaining units were delivered together, resulting in two sets of files for each sample.