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

• Main Authors: Cohen, Natalie, Krinos, Arianna, Alexander, Harriet, Saito, Mak
• Format: Other/Unknown Material
• Language: English
• Published: Zenodo 2024
• Subjects: metatranscriptome; protists; ocean; microbes; North Atlantic
• Online Access: https://doi.org/10.5281/zenodo.12789183

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 using4 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 taxonomicannotations 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-spectrummatches 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) ...