TnSeq of P. mirabilis from in vitro growth in LB or serum
Bacterial genomic DNA was isolated from P. mirabilis in the inputs and serum samples by hexadecyltrimethyl ammonium bromide (CTAB) precipitation. Samples were enriched for transposon insertion junctions as outlined by Goodman et al. (Nat Protoc 2011). TapeStation analysis was used to confirm concentration and purity, and samples were multiplexed and subjected to V4 single end 50 HiSeq-2500 High-Output sequencing. Input samples and serum samples (2 replicates each) were multiplexed and sequenced on a single lane. Each lane was spiked with 15% bacteriophage X DNA to overcome low-diversity sequences. Sequencing was performed at the University of Michigan DNA core facility.