During the expedition PS136 LTER HAUSGARTEN in 2023 105 samples of macrobenthic marine invertebrates and 3 samples of calanoid copepods were collected by epibenthic sledge and 28 samples of calanoid copepods were collected by Bongo and Multinet and subsequently frozen at -80 degrees Celsius for lipid and bulk stable isotope analyses. Katrin Linse, Saskia Brix, Jannifer Freer and Lydia Anastasia Schmidt collected, photographed and fixed the specimens on board. The macrobenthic invertebrates and calanoid copepods were collected to study elements of the biological lipid pump in the Arctic Ocean. The preparation and lab analyses of the lipid biomarker and stable isotope data were carried out by Rachel Jeffreys and Sabena Jane Blackbird at the University of Liverpool using Gas chromatography-mass spectrometry and an ECS8020 elemental analyser (NC Technologies) coupled to a Delta V isotope ratio mass spectrometer. Statistical analyses and interpretation of lipid biomarker and stable isotope data were carried out by Dewi Ford, Dan Mayor and Anna K. Wadsworth at the University of Exeter. The raw data files include lipid biomarker and stable isotope data for all analysed macrobenthic invertebrates and calanoid copepods, while the processed data files include all calanoid copepod data but selected macrobenthic taxa only, being Amphipoda, Decapoda, Isopoda, Mysidacea, Holothuroidea, Ophiuroidea, and Chaetognatha. The contributions of KL, JF and DJM were supported by the BIOPOLE National Capability Multicentre Round 2 funding from the Natural Environment Research Council (grant no. NE/W004933/1). DJM also received funding from OceanICU (EU Grant agreement ID: 101083922; UKRI grant reference: 10063673). SB received support via the Leibniz foundation and the ALONGate project (A Long-term Observatory of the North Atlantic Gateway to the Arctic Ocean) via grant number PS150/2023 in the program for women professors. The field work for PS136 was supported by grant no. AWI_PS136_01.

At the basis of the marine Arctic food web, there are several carbon sources including ice-associated (sympagic) algae that live primarily in sea ice, melt ponds or underneath sea ice; pelagic algae that live primarily in open waters; terrestrial detritus that got incorporated into sea ice forming on the Siberian Shelf and being transported with the transpolar drift across the Central Arctic Ocean (CAO); and detritus that derives with currents from the Atlantic ocean. Copepods and amphipods are diverse and often biomass-dominant zooplankton groups in the CAO that include taxa specialised in feeding on algae and small heterotrophs, on sinking detritus or other zooplankton. Gelatinous (cnidaria, appendicularia) and semi-gelatinous (chaetognaths) taxa, ostracods, pteropods, euphausiids and pelagic decapods are other important zooplankton groups in the CAO that likewise feed on a range of food sources. With the loss of Arctic sea ice, the relative importance of ice-associated carbon in the Arctic food web became a central research topic, and multiple trophic marker approaches have been developed to distinguish between pelagic and sympagic carbon transfer to higher trophic levels. During the MOSAiC expedition in the CAO (2019-2020), zooplankton was sampled weekly to fortnightly. A range of nets were used to sample either horizontally underneath the sea ice or vertically from a maximum depth of 2000 m to the surface. Onboard, abundant zooplankton taxa were sorted from each catch, photographed, rinsed with freshwater to remove salt and frozen at -80 degrees Celsius for subsequent analysis of their total dry mass (DM), lipid content, lipid classes and a suite of trophic markers, including bulk stable isotopes (BSI), phytosterols (PS), total fatty acids (TFA), total fatty alcohols (TFAlc), highly-branched isoprenoids (HBI) and the carbon isotopic composition of key FA and FAlc (CSIA-FA; CSIA-FAlc). We had ~10 target species that were sampled in all seasons (the copepods C. hyperboreus, C. glacialis, Metridia longa, the ice amphipods Apherusa glacialis and Eusirus spp., the pelagic amphipods Themisto abyssorum and T. libellula, the euphausiid Thysanoessa spp., chaetognaths and the shrimp H. glacialis). Further zooplankton taxa were collected when available in the net catches and time permitted. Additionally, Polar cod was collected in early and late summer. The initial separation of the various trophic markers was carried out at the University of Plymouth. After estimating the total DM, subsamples for BSI were sent to the Littoral, Environment and Societies Joint Research Unit stable isotope facility (CNRS - University of La Rochelle, France) for analysis. Three internal standards were added to the samples used for lipid analysis to quantify the TFA, TFAlc, PS and HBI content. As a first step, the total lipid content of the animals was extracted in dichloromethane : methanol. The lipid samples were split into two equal subsamples, one was sent to the Alfred-Wegener-Institute (AWI) in Bremerhaven/Germany for FA and FAlc analyses and the second was used for PS and HBI analyses in Plymouth. This dataset is linked to a manuscript that assesses trophic relationships in the CAO to understand the carbon fluxes in the current Arctic food web and to predict potential changes in a future ice-free Arctic. Contributions by KS were funded by the UK's Natural Environment Research Council MOSAiC Thematic project SYM-PEL: "Quantifying the contribution of sympagic versus pelagic diatoms to Arctic food webs and biogeochemical fluxes: application of source-specific highly branched isoprenoid biomarkers"/ (NE/S002502/1). CJA, RGC, CEG, KMS and RJ were funded by the US National Science Foundation Office of Polar Programs (OPP-1824447 and OPP-1824414).