Sediment cores were collected onboard the CCGS Amundsen during ArcticNet cruise 0502 (2005) using a box corer, penetrating the seafloor to a maximum of 50 cm. Samples were stored in a freezer (- 20 °C) onboard the Amundsen until the end of the cruise, then shipped to the Freshwater Institute (FWI), where they were maintained in storage at - 20 °C. Subsamples were processed at the University of Victoria Marine Micropaleontology Laboratory in October-November 2010. A gentle version of the standard palynological protocol was applied to oven-dried samples of known volume. Steps are as follows: (1) add 10 % hydrochloric acid in room temperature; (2) sieve with distilled water through a 120 micrometre and a 15 micrometre nitex mesh, retaining the fraction in between; (3) add 48% hydrofluoric acid in room temperature for 2-4 days followed by 20 minutes in 10 % hydrochloric acid; (4) sieve through precise 15 micrometre mesh with gentle sonication for 10-60 seconds. The final residue of samples was placed in sealed storage vials and stored in + 4 °C. Aliquots of residue were mounted in glycerine jelly on microscopic slides with cover slips. Dinoflagellate cysts are studied primarily with Zeiss Standard 20 microscope under bright-field oil-immersion and 500X and 1000X magnifications. At least 300 dinoflagellate cysts species and cyst types will be identified on each slide together with pollen, freshwater algae and other palynomorphs.

Free-drifting, short-term particle interceptor traps were deployed from the CCGS Amundsen on eight occasions between 23 September and 16 October 2005. The traps were deployed at two or three depths below the euphotic zone (from 25 to 150 m) for 8 to 20 h. The sinking material was analyzed for particulate inorganic carbon, particulate and dissolved organic carbon, biogenic and lithogenic silica and chlorophyll a concentrations. Phytoplankton abundance and composition, fecal pellet abundance and biovolume and bacterial abundances were also assessed for the sinking material. Water column samples, from depths between 10 and 150 m, were collected to quantify fecal pellets. Lastly, phytoplankton from the deep chlorophyll maximum depth was collected and their sinking velocity determined using settling columns.

Zooplankton (Calanus sp., Limacina helacina, Euphasiacea, Clione limacina, Themisto sp., Paraeuchaeta sp, Hyperoche sp. and Sagitta sp.) were collected in net tows during 2003 & 2004 (onboard the CCGS Pierre Radisson and Des Groseillers) and 2005 & 2010 (onboard the CCGS Amundsen). After taxonomical sorting, samples were frozen for chemical analysis. Total mercury (THg) analysis was conducted at the Freshwater Institute, Winnipeg (DFO) using cold vapor atomic absorpotion spectrometry; monomethylmercury (MMHg) was analyzed at the University of Ottawa using gas chromatography atomic fluorescence spectroscopy; stable isotope ratios of nitrogen and carbon were run at the University of Winnipeg Isotope Laboratory using continuous flow ion ratio mass spectrometry.

Agassiz trawl was deployed from the CCGS Amundsen to collect macrofauna. Catches were passed through a 2 mm mesh sieve. When possible, specimens were identified to the lowest taxonomic level, then count and weight. The unidentified specimens were preserved in a 4% seawater-formalin solution. Box corer was deployed to quantitatively sample diversity, abundance and biomass of infauna and to sample sediment. Sediments of a surface area of 0.125 m2 and 10-15 cm in depth were collected and sieved through a 0.5 mm mesh and preserved in a 4% formaldehyde solution for further identification in the laboratory. Sub-cores of sediments were collected for sediment pigment content, organic matter, sediment grain size, porosity; for sediment pigments, the top 1 cm was collected, although for sediment grain size, the top 5 cm was collected. Sediment pigment samples were frozen at -80°C, and porosity, organic matter and sediment grain size samples were frozen at -20°C.

The CTD data was obtained during the 2010 ArcticNet scientific cruise #1001a. The data were collected from July 7 to 31, 2010, aboard the CCGS Amundsen. There were 66 casts associated to 40 stations, located in the Hudson Bay and Hudson Strait research areas. The following parameters were measured: temperature, conductivity and pressure (with a Sea-Bird SBE-9plus), dissolved oxygen (Sea-Bird SBE-43), fluorescence (Seapoint chlorophyll fluorometer), CDOM (Wetlabs FL(RT)D), nitrate concentration (Satlantic MBARI-ISUS 5T), transmittance (Wetlabs C-Star transmissometer), light intensity (PAR; Biospherical Instruments QCP2300) and surface light intensity (sPAR; Biospherical Instruments QCP2200). Quality control procedures were applied to the data. Data are available on the Polar Data Catalogue and at the Marine Environmental Data Service (MEDS) of Fisheries and Oceans Canada.

The Canadian research icebreaker CCGS Amundsen is equipped with a Moving Vessel Profiler (copyright) (MVP), a multi-purpose instrument used to collect both shallow and deep water data sets, without the need to stop the vessel. Data on physical and chemical characteristics of the water column are collected during transects along which several consecutive casts of the MVP are conducted. The MVP was deployed during the Amundsen scientific expeditions, in the summer and fall of 2004 to 2018 with the exception of 2005 and 2006, where no data is available, and 2012 because the ship was undergoing maintenance. The components of the system varied slightly throughout the year but typically included a Micro CTD (Temperature, Conductivity and Pressure), a Micro DO2 (Dissolved Oxygen), a Micro SV (Sound velocity and Pressure) and an ECOFLO (Fluorescence) and a C-Star (Transmittance) probe. The MVP data were corrected and then controlled by comparing them to CTD-Rosette and thermosalinograph (TSG) data when available. Variables are provided for every decibar (dbar) between the maximum and minimum pressure recorded for each cast. Detailed metadata and reports are included to provide more information.