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