Metatranscriptomic assembly, predicted open reading frames, counts, and annotation files from seawater samples obtained in the western North Atlantic Ocean. GitHub notebooks are located here: https://github.com/cnatalie/BATS. Assembly was created using the eukrhythmic pipeline: https://github.com/AlexanderLabWHOI/eukrhythmic merged_merged.fasta.gz = Final assembly, merged across 44 metatranscriptomes using 4 different assemblers merged.fasta.transdecoder.pep.zip = Open reading frames of final assembly, predicted by Transdecoder merged.fasta.transdecoder-estimated-taxonomy.out.zip = EUKulele-derived taxonomic annotations of ORFs using a combined EukProt, PhyloDB, and RefSeq reference database newtaxa.eukprot.merged.fasta.transdecoder-estimated-taxonomy.out.zip = similar to above, but manually curated mid-level taxonomy for supergroups of interest eggnog.emapper.annotations.zip = eggnog-mapper annotations of ORFs table.tab.zip = counts associated with ORFs (merged.fasta.transdecoder.pep) generated with Salmon TPM_table.tab.zip = community-wide TPM (normalized) counts associated with ORFs (merged.fasta.transdecoder.pep) generated with Salmon copiesperL.tab.zip = raw counts associated with ORFs (merged.fasta.transdecoder.pep) converted to copies per L using spiked-in RNA standard concentration (copies), standard reads mapped, and volume of seawater filtered assembly.table.tab.zip = counts associated with final assembly (merged_merged.fasta) generated with Salmon SamplesViewReportCLIO_AE1913merged_trans210506_updated220606exclusive.zip = Exclusive spectral counts associated with ORFs (merged.fasta.transdecoder.pep). Peptide-spectrum matches were performed using Sequest algorithm within IseNode Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific). Scaffold 5.1.2 (Proteome Software) was used for protein grouping and exclusive spectral counting. Note, the (+x) data has been removed from protein names, which indicates whether (and how many) proteins sharing peptides were designated into the same protein group. cds.length2.tab.zip = Length of proteins (ORFs) in nucleotide base pairs CTD.zip = CTD files from cruise AE1913