Dataset: Transcriptomic expression data from cultures of Alteromonas macleodii MIT1002 grown with bacterial extracellular vesicles as a carbon source

This lab experiment was conducted at Wellesley College, Welleslsey MA in August 2024. Alteromonas macleodii MIT1002 were grown at 24 °C in a natural seawater-based media containing 0.2 µM filtered, autoclaved seawater supplemented with 3 mM NH₄Cl, 50 µM NaH₂PO₄, Pro99 trace metals, and 0.01% (w/v) glucose. Overnight cultures of Alteromonas were washed twice in media lacking added glucose (-C). Cultures were diluted to 5e6 cells/mL and supplemented with with either 1x PBS (negative control), Prochlorococcus extracellular vesicles, Alteromonas extracellular vesicles, or glucose as a carbon source, each in triplicate. Cultures were incubated at 24°C with shaking at 120 rpm. Samples were collected at two timepoints (representing early and late exponential growth phase) by pelleting at 10,000 xg for 15 minutes, flash freezing on dry ice, and storing at -80 °C. Cells were resuspended and lysed in 600 µL Zymo TriReagent and RNA was extracted using the Zymo Trizol RNA Extraction RNA spin column kit following the manufacturer’s protocol. The columns were washed and treated with DNAse per manufacturers recommendation. RNA was eluted in 50 µL of RNase-free water and quantified using the Qubit RNA High Sensitivity kit (Invitrogen). Ribosomal RNA was depleted using the Qiagen QIAseq FastSelect kit, then the Kapa RNA Hyperprep kit. Paired-end 150nt sequencing data was generated on an Illumina NovaSeq X. RNA library preparation and sequencing was carried out by the  Bauer Core Facility (Harvard University).