Samples were collected from nine sites distributed across the study region in 2008 and 2009. To avoid confounding influence of seasons, the same sites were sampled in the same season each year. Sampling was conducted onboard the CCGS Amundsen between July and October during the Circumpolar Flaw Lead Study, ArcticNet expeditions in collaboration with the Canadian Healthy Ocean Network and the Malina project. Locations were chosen to study both hotspots and coldspots in the Canadian Arctic. At each sampling station, an USNEL box corer was deployed for seafloor sediment collection. From each box core, three to five sub-cores of 10 cm diameter and approximately 20 cm sediment depth were taken for assessing benthic remineralisation function in shipboard microcosm incubations. After incubation, the same sediment cores were passed through a 0.5 mm mesh sieve under slow running seawater. The sieve residues were preserved in a 4% seawater-formaldehyde solution for later analyses of species diversity and abundance under a dissection microscope.

Continuous air samples were collected on Legs 8 and 9 of the CCGS Amundsen cruise in 2008 using a high volume air sampler that drew air through a glass fibre filter followed by two polyurethane foam plugs. Water samples were collected by filter water through a glass fibre filter followed by a solid phase absorbent. Samples were extracted back at the laboratory followed by analysis using a gas chromatograph-mass spectrometer. Data generated included concentration of semi-volatile contaminants in air and water and chiral signature of chiral components.

The CTD data was obtained during LEG 04 of the 2004 CASES scientific cruise #0401. This Leg was carried out from January 7th 2004 to February 18th 2004 aboard the CCGS Amundsen. There were 119 CTD casts in Leg 4. All of these casts, associated to the overwintering oceanographic station, are located in Beaufort Sea research area. The following parameters were measured: temperature, conductivity and pressure (with a Sea-Bird 911 probe), oxygen (Sea-Bird 43), pH (Seabird 18), fluorescence (Seapoint fluorometer), nitrates (Satlantic MBARI ISUS), transmittance (Wetlabs C-Star transmissometer), PAR/Irradiance and SPAR/Irradiance (Biospherical Instruments QC2300). Data were quality controlled. Data are available on the Polar Data Catalogue and at the Marine Environmental Data Service (MEDS) of Fisheries and Ocean Canada.

Real-time atmospheric measurements were made on board the CCGS Amundsen. Sampling lines were placed on the forward mast of the ship, and instruments were housed in a sampling shed located on the top deck. Mixing ratios of volatile organic compounds (VOCs: dimethylsulfide, acetone, methanol, benzene, etc.) were measured using proton-transfer-reaction mass spectrometry. Aerosol size distributions between 10 and 500 nm were measured using a scanning mobility particle sizer and total aerosol number concentrations > 3 nm were measured using an ultrafine condensation particle counter. All data have time resolution of minutes.

As part of the ArcticNet expeditions (http://www.arcticnet.ulaval.ca) on the CCGS Amundsen in 2008-2019, we collected water samples from stations throughout the Canadian Arctic. Cruise tracks varied from year to year, but always included a transect of northern Baffin Bay, and sometimes sampling in Lancaster Sound, the Beaufort Sea, and/or along the east coast of Baffin Island. The sampling period ranged from summer to autumn. Samples were collected by CTD-rosette from 2-8 depths corresponding to water column features such as surface water, the subsurface chlorophyll maximum, the nitracline, or Atlantic Water. To collect samples for DNA/RNA, water was filtered through 3-µm filters and 0.2 µm cartridges, which were conserved in a buffer at -80°C. These have been used for high-throughput sequencing for amplicon-based surveys, metagenomics, and other molecular techniques. Samples for flow cytometry (to enumerate bacterial and/or pigmented cells), microscopy (with a fluorescent DAPI stain, or using FNU preservative for identifying larger cells), fluorescent in-situ hybridization (another microscopy technique), chlorophyll a (to quantify photosynthetic organisms), and HPLC pigment analysis (to identify different algae taxa), were also collected. Samples from which nucleic acids have been extracted and sequenced in many projects. Samples from which nucleic acids have been extracted and sequenced can be found in the GenBank Short Read Archive under the project accession numbers PRJNA202104, PRJNA283142, PRJNA283296, PRJNA383398, and SRX037894-SRX037896

Sampling took place on legs 6, 7, 8b, and 9 of the CFL project on the CCGS Amundsen (2008). Zooplankton were sampled with a 1x1m2 (200 µm mesh) net through the moon-pool and with a 1m diameter (200 µm mesh) ring net on the ice at ice covered stations. In open water, samples were collected with 2x1 sq.m (500 µm mesh), 4x1 sq.m (500 and 200 µm mesh), and rectangular mid-water trawl (1600 µm mesh). Samples were live sorted to species and frozen at -25C. Algae were collected from the bottom ice via ice cores and the dive program, from the ice interface/surface water with a Hg clean Niskin and a hose and pump on a 1m arm, and from the chlorophyll a maximum depth via the rosette. Samples in ice were frozen in the dark, while samples in water were filtered via dual filtration following Morrison and Watras (1999) and filters were frozen at -25C. Zooplankton species Calanus glacialis and Calanus hyperboreus were analyzed for total mercury using CVAAS; C. hyperboreus was also analyzed for methyl mercury via Gas Chromatography Atomic Fluorescence Spectrophotometry (GC AFS). The algae samples were analyzed for THg using cold vapour atomic absorption spectrometry (CVAAS) and MeHg using cold vapour atomic fluorescence spectroscopy (CVAFS).

This data is currently in relation to twelve piston cores collected aboard CCGS Amundsen, one on cruise 2014805, two on cruise 2015805, six on cruise 2016804, and three on cruise 2017805. Information about these cores (Location, length, grain size, radiocarbon dates, etc.) can be found by searching the NRCan Expedition Database.

During the ArcticNet annual cruises of the research icebreaker CCGS Amundsen, characteristics of the near-surface atmosphere (basic meteorological elements, incident radiation, CO2 concentration) are monitored in conjunction with surface sea water properties (temperature, salinity, dissolved CO2 and O2) to observe the relationship between the surface micro-climate and the air-sea exchange, with particular interest in CO2. Central to this integrated dataset, the following meteorological variables were recorded at 1 minute intervals (instrument used to collect each variable is in parentheses, and approximate instrument height above surface is indicated): -Wind speed (RM Young Wind Monitor 05103) - 16m height -Wind direction (RM Young Wind Monitor 05103) -16m height -Air Temperature (Vaisala HMP45C212) - 15m height -Relative Humidity (Vaisala HMP45C212) -15m height -Surface temperature (Everest IR Transducer, 4000.44ZL) - 8m height All instruments were mounted on a meteorological tower on the bow of the research icebreaker CCGS Amundsen.

As part of this project, the following variables were measured continuously at 1 minute intervals using a custom-built pCO2 equilibrator attached to the ship's clean water intake: -pCO2sw (LI7000 gas analyzer) -Equilibrator water temperature

Water samples were collected at approximately 0.3 m depth at all stations in Hudson Bay during the the 2010 cruise from Kuujjuarapik, PQ to Churchill, MB. We collected samples at basic, mooring and CTD (conductivity-temperature-depth) stations, as well as along two transects made by Zodiac near the mouth of the Rivière de la Grande Baleine and off Cape Tatnam, located at ca. 100 km East of the Nelson River. All water samples were filtered on board, and subsamples were retained for analysis for dissolved and particulate organic carbon and nitrogen, as well as for phosphate, total soluble salts (TSS), chlorophyll a, CDOM (absorbtion and fluorescence spectra), oxygen-18 and salinity. At each station, water column profiles were recorded, each to the bottom or at least 30 m depth, using an Idronaut CTD with conductivity, temperature, depth and turbidity sensors, and a WetLabs ECO Fluorometer for CDOM fluorescence. In addition,we made several water column profiles of absorption and attenuation spectra off the mouth of the Rivière de la Grande Baleine, using a WetLabs hyperspectral absorption and attenuation meter (WetLabs acs). We also recorded miscellaneous water surface reflectance spectra, using a Satlantic HyperSAS instrument mounted on the ship's bow, near Rivière de la Grande Baleine, near the mouth of James Bay and in the outer estuary of the Nelson River.