10.1594/PANGAEA.921026Käse, LauraLauraKäse0000-0003-0632-0729Kraberg, Alexandra ClaudiaAlexandra ClaudiaKraberg0000-0003-2571-2074Metfies, KatjaKatjaMetfiesNeuhaus, StefanStefanNeuhaus0000-0001-8245-1486Sprong, PimPimSprongFuchs, Bernhard MBernhard MFuchs0000-0001-9828-1290Boersma, MaartenMaartenBoersma0000-0003-1010-026XWiltshire, Karen HelenKaren HelenWiltshire0000-0002-7148-0529PANGAEA2020DNA barcodingeukaryotic planktonOTUPhytoplanktonprotistsZooplanktonBinary ObjectDataset10.1093/icesjms/fsab05810.1371/journal.pone.02448172 data pointstext/tab-separated-valuesCreative Commons Attribution 4.0 InternationalWater samples were collected from the long-term ecological research (LTER) site at Helgoland and the eukaryotic microbial community was assessed. 18S V4 region was amplified using the primer set 528iF /964iR and amplicon sequencing was performed on an Illumina MiSeq™ sequencer in a 2 × 300 bp paired-end run. Sequence data have been deposited in the European Nucleotide Archive (ENA) at the European Bioinformatics Institute (EMBL-EBI) under accession number PRJEB37135 using the data brokerage service of the German Federation for Biological Data (GFBio). 21 million sequences remained after bioinformatic processing and were clustered into Operational Taxonomic Units (OTUs). The Protist Ribosomal Reference database (PR2), version 4.11.1 was used as reference database.7.954.188German Bight, North Sea