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This dataset provides an inventory of physical samples collected from zooplankton bongo and/or ring net tows conducted during the Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises, ongoing since 2018. The NES-LTER transect, located south of Martha’s Vineyard, Massachusetts, comprises standard stations L1-L11 and extends 150 km offshore. Dedicated NES-LTER cruises target all four seasons: winter, spring, summer, and fall. Samples are collected via oblique tows with a 61-cm bongo net fitted with 150- and 335-micron mesh nets, as well as a ring net with a 20-micron mesh net. During earlier spring and fall cruises along the NES-LTER Transect, in collaboration with the Ocean Observatories Initiative, samples were collected through vertical tows using a ring net with a 150-micron mesh. Samples collected are distributed among various laboratories for DNA metabarcoding, stable isotopes analysis, and morphological identification. 

This data package provides abundance data for zooplankton collected during seasonal transect cruises conducted as part of the Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) program, ongoing since 2018. Zooplankton are collected at standard NES-LTER transect stations (L1–L11) and the Martha’s Vineyard Coastal Observatory (MVCO) via oblique tows, using a 61-cm Bongo net with two mesh sizes (335 µm and 150 µm). The transect extends southward from near Martha’s Vineyard, Massachusetts, reaching approximately 150 km offshore along longitude 70 deg 53 min W, covering the continental shelf from nearshore to the shelf break, with sampling depths between 20 and 200 meters. Only the 335-µm mesh data is included here, as samples from this net are preserved on board and shipped to Morski Instytut Rybacki in Szczecin, Poland, where they are counted and identified to the lowest possible taxonomic level. Counts of taxa identified are provided by the NOAA’s Northeast Fisheries Science Center. Samples from the 150 um are preserved for other purposes and will be published as a separate data package. This second version of the data package includes staged and unstaged abundance data in volumetric (100 m³) and aerial (10 m²) units from the 335-µm net. Supplemental tables provide metadata for the cruises and stations.