Protistan metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

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_ORFs_FactorIncluded.csv.zip = raw counts associated with ORFs (merged.fasta.transdecoder.pep) converted to copies per L taking into account spiked-in RNA standard concentration (copies), standard reads mapped, volume of seawater filtered, and dilution factor used in library preparation
• 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