Dataset: Metadata for transcriptomic expression data from cultures of Ruegeria pomeroyi DSS-3 and Alteromonas macleodii MIT1002 grown in defined culture media with either glucose, acetate, or a mix of both as carbon substrates

This lab study took place in Athens, Georiga (GA), USA within the Department of Marine Sciences at the University of Georgia. Experiments were conducted on several dates: samples ending in _glc_a/b/c (samples grown with glucose only) were collected February 22-23, 2022; samples ending in _ac_a/b/c (samples grown with acetate only) were collected June 24-25, 2022; and the rest of the samples ending with _glc_ac_5/8/19/34_a/b/c (grown with both glucose and acetate) were collected July 16-17, 2022.

Samples were collected for transcriptomic analysis during exponential growth phase from liquid cultures, and samples were pelleted and immediately frozen at -80°C. RNA was extracted from thawed samples using the Zymo Quick-RNA Fungal/Bacterial Microprep kit (Irvine, CA, USA). Ribosomal RNAs were depleted using NEBNext® rRNA Depletion Kit (Ipswich, MA, USA), and the remaining RNA was purified using the Zymo RNA Clean and Concentrator-5 kit (Irvine, CA, USA). RNA concentration was quantified using Qubit fluorometry (Invitrogen, Waltham, MA, USA), and libraries were prepped using the NEBNext® Ultra™ II Directional RNA Library Prep kit (Ipswich, MA, USA). Sequencing was conducted at the Georgia Genomics and Bioinformatics Center (Athens, GA, USA) using the Illumina NextSeq 2000 platform to obtain 50-bp single-end reads.