Thalassiosira pseudonana were removed from the co-cultures by pre-filtration through 2.0 µm pore-size filters, and bacteria were collected on 0.2 µm pore-size filters. Filters were incubated in SDS (0.6% final concentration) and proteinase K (120 ng μl –1 final concentration). RNA was extracted from duplicates of each treatment by adding an equal volume of acid phenol:chloroform:isoamyl-alcohol, followed by shaking, centrifugation, and collection of the supernatant. A second extraction was carried out by the addition of an equal volume of chloroform:isoamyl-alcohol. RNA was recovered from the supernatant, treated to remove rRNA, and sequenced.

Each sequence library is from four independent bacterial samples that were pooled for sequencing. The data are assigned to one of the four samples post-sequencing by mapping to the genomes of each of the four bacteria. The data table provides the accession numbers of the bacterial genomes to be used for mapping in the final column.