The dataset is composed of Ichthyoplankton and zooplankton captured during the ArcticNet cruise aboard the CCGS Amundsen from 2017 to 2019. Three samplers fitted with 200 µm to 500 µm mesh nets were used for zooplankton collection . One was a metallic structure with 4 nets of 1 square meter opening each (2x2 multiple net sampler) for water column integrated sampling pulled vertically over from 10 m above the bottom to the surface to catch mesozooplankton. The other sampler was 2 nets of 1 square meter opening each towed at 10 m depth for 20 minutes at 2 knots to catch ichthyoplankton and macrozooplankton. Finally, a 0.5 square meter opening multinet Hydrobios for stratified sampling into nine layer also hauled vertically from 10 m above the sea bottom to the surface. Zooplankton samples were preserved in a 10% buffered formalin seawater solution and were sieved through 1000 µm and 200 µm sieves for analysis. Ichthyoplankton was identified to the lowest taxonomic level possible, a sub-sample was measured and all larvea were kept in ethanol.

Multibeam echosounder data near Qikiqtarjuaq were collected by the CCGS Amundsen in 2007 and by the RV Nuliajuk from 2012-2015. Data collected between 2007 and 2014 were processed by the Ocean Mapping Group at the University of New Brunswick (http://www.omg.unb.ca/) and were retrieved from their data sharing interface (http://www.omg.unb.ca/Projects/Arctic/SE_Baffin/). Data collected in 2015 were processed by the Fisheries and Marine Institute at Memorial University of Newfoundland (https://www.mi.mun.ca/) and were obtained directly from them. These datasets were clipped to only include the area near Qikiqtarjuaq relevant to the benthic habitat mapping project lead by the Memorial University Marine Habitat Mapping Group. Individual datasets were mosaicked to create single continuous bathymetry (m) and backscatter (dB) raster layers at 5 m resolution. Mapping activities were funded by ArcticNet and the Government of Nunavut, Department of Environment, Fisheries and Sealing Division to support benthic habitat mapping for marine ecosystem management in this area.

Benthic grab samples and underwater towed video samples were collected at long-term ecology sites while onboard the Government of Nunavut vessel MV Nulialjuk and CCGS Amundsen in July and October 2016. On-board the MV Nulialjuk, benthic grab samples (triplicate samples) and underwater towed video samples were collected at 5 long-term ecology stations near Iqaluit. An additional 7 benthic grab samples (triplicate samples) and towed video samples were collected near Cairn Island. On-board the CCGS Amundsen, benthic grab samples were collected at two long-term ecology stations (triplicate samples) near Cairn Island. Sampling gear included a Van Veen grab sampler, box core, and HD GoPro video system. Initial observations suggest that these stations are predominantly muddy sand with some larger cobbles present. Towed video analysis and benthic grab samples indicate the presence of the algae Laminaria sp. and Agarum clathratum and bivalves Mya truncata, Yoldia hyperborea, Clinocardium ciliatum, and Serripes groenlandicus. Ophiuroid echinoderms and tubiculous polychaete worms and tubes are abundant. Once all benthic grab samples and towed video samples are processed, this data will be compared with the historic sample data to answer questions about the nature of long-term change of the benthos at this region in inner Frobisher Bay.

Bottom water (20 L per station) was collected at 11 stations in Baffin Bay using the CCGS Amundsen’s rosette system. Water was filtered aboard the vessel into glass microfiber (GF-F) filters for Carbon and Nitrogen stable isotopic composition analysis. These data will be used in combination with data on soft coral stable isotopic composition collected from the same region.

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.

First-year sea ice was sampled on 36 occasions near the overwintering site of the CCGS Amundsen during the Canadian Arctic Shelf Exchange Study (CASES). Sea-ice and associated surface water samples were taken every 3 to 5 days between 24 February and 20 June 2004. Surface waters and the bottom 3-5 cm of ice cores were routinely analyzed for: salinity, pH, nutrients (NH4, NO2, NO3, Si(OH)4, and PO4), dissolved organic carbon and nitrogen (DOC, DON), exopolymeric substances (EPS), particulate inorganic carbon (PIC), particulate organic carbon and nitrogen (POC, PON), total and >5 µm chlorophyll a and phaeopigments, bacterial abundances/biomass, protist (excluding diatoms) abundances/biomass and ice algal/phytoplankton taxonomy. This data set also includes vertical and spatial profiles of ice algal distribution as well as measurements of sea-ice primary production, bacterivory and sea-ice algal and bacterial sinking velocities.

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

Our sampling program took place from August 27, 2009 through September 12, 2009. It was part of Leg 3a of the 2009 CCGS Amundsen Expedition in the Arctic Ocean (ArcticNet 0903). Sampling started in the Mackenzie River delta and continued into the Beaufort Sea (Shelf, slope and deep Canada Basin). Various measurements (temperature, salinity, nutrients, alkalinity, pH, primary production, bacterial production) and sampling (seawater, marine particles) were conducted at 10 stations. Underway measurements (temperature, salinity, trace gases) and sampling (marine particles) were also conducted along the cruise track. Sampling tools on stations were the ship's CTD/rosette (ArcticNet), a Trace-Metal CTD/rosette system (UVic / UBC) and large volume in-situ pumps (UBC). We conducted measurements and collected samples to document a suite of key physical (temperature, salinity, ice cover, light penetration), chemical (nutrients, trace metals, trace gases, radioisotopes, stable isotopes) and biological (phytoplankton and microbial assemblages, primary and microbial productivity, trace metal phytoplankton quotas) parameters in relation to proximity to the Mackenzie River delta, seafloor bathymetry and ice cover to elucidate the processes influencing phytoplankton growth and carbon cycling in the Arctic Ocean. In particular, we collected samples to study the processes which supply and remove trace metals, nutrients and carbon to and from the upper ocean, and conducted ship-board experiments to study how biological productivity is affected by various chemical and physical conditions. Through a combination of on-board measurements, experiments and subsequent laboratory analysis, our research program aims at: (i) documenting the pathways of addition, removal and cycling of key trace elements which act as biological micronutrients or tracers of carbon and nutrient cycles in the Arctic Ocean; (ii) elucidating the potential effects of changing ice cover and river discharge on productivity, carbon sequestration and trace gas emission in the Arctic Ocean; (iii) developing chemical tracers to establish a historical sedimentary record of Arctic Ocean productivity in relation to long term natural climate change.