cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7317271
title: Protistan metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

description: Metatranscriptomic assembly, predicted open reading frames, counts, and annotation files from seawater samples obtained in the western North Atlantic Ocean. GitHub notebooks are located here: https://github.com/cnatalie/BATS. Assembly was created using the eukrhythmic pipeline: https://github.com/AlexanderLabWHOI/eukrhythmic



merged_merged.fasta.gz = Final assembly, merged across 44 metatranscriptomes using 4 different assemblers

merged.fasta.transdecoder.pep.zip = Open reading frames of final assembly, predicted by Transdecoder 

merged.fasta.transdecoder-estimated-taxonomy.out.zip = EUKulele-derived taxonomic annotations of ORFs using a combined EukProt, PhyloDB, and RefSeq reference database

newtaxa.eukprot.merged.fasta.transdecoder-estimated-taxonomy.out.zip = similar to above, but manually curated mid-level taxonomy for supergroups of interest

eggnog.emapper.annotations.zip = eggnog-mapper annotations of ORFs

table.tab.zip = counts associated with ORFs (merged.fasta.transdecoder.pep) generated with Salmon

TPM_table.tab.zip = community-wide TPM (normalized) counts associated with ORFs (merged.fasta.transdecoder.pep) generated with Salmon

copiesperL_ORFs_FactorIncluded.csv.zip = raw counts associated with ORFs (merged.fasta.transdecoder.pep) converted to copies per L taking into account spiked-in RNA standard concentration (copies), standard reads mapped, volume of seawater filtered, and dilution factor used in library preparation

assembly.table.tab.zip = counts associated with final assembly (merged_merged.fasta) generated with Salmon

SamplesViewReportCLIO_AE1913merged_trans210506_updated220606exclusive.zip = Exclusive spectral counts associated with ORFs (merged.fasta.transdecoder.pep). Peptide-spectrum matches were performed using Sequest algorithm within IseNode Proteome Discoverer 2.2.0.388 (Thermo Fisher Scientific). Scaffold 5.1.2 (Proteome Software)  was used for protein grouping and exclusive spectral counting. Note, the (+x) data has been removed from protein names, which indicates whether (and how many) proteins sharing peptides were designated into the same protein group. 

cds.length2.tab.zip = Length of proteins (ORFs) in nucleotide base pairs

CTD.zip = CTD files from cruise AE1913
DOI: 10.1594/pangaea.807188
title: (Table 1) Paleomagnetism at DSDP Leg 81 Holes

description: Paleomagnetic data are tabulated for DSDP Sites 552, 553, 554, and 555, drilled on the southwest margin of Rockall Plateau. No interpretation of these data has been given; because the results provide a particularly valuable record of Paleogene and Neogene magnetostratigraphy they have, however, been provided here for use by the community.
description: Supplement to: Krumsiek, Klaus A O; Roberts, David G (1984): Paleomagnetics of Tertiary sediments from the Southwest Rockall Plateau, Deep Sea Drilling Project Leg 81. In: Roberts, DG; Schnittker, D; et al. (eds.), Initial Reports of the Deep Sea Drilling Project, Washington (U.S. Govt. Printing Office), 81, 837-851
DOI: 10.1594/pangaea.892959
title: Biogeochemical redox proxies in sediments from Schandelah during the Toarcian (Early Jurassic)

description: Author contributions:The sampling was led by Bas van de Schootbrugge and measurements performed by Nina Papadomanolaki, with supervision of Niels A. G. M. van Helmond and Caroline P. Slomp. Measurements were gathered, processed and analysed by Itzel Ruvalcaba Baroni.
DOI: 10.1594/pangaea.511106
title: Radiosonde at Georg-Forster station on 1988-01-06 12:00h

description: Height of tropopause 9531 m, total ozone 278.3 DU
DOI: 10.1594/pangaea.807225
title: (Table 1) Egg laying and hatching dates and guarding duration of Adélie penguins (Pygoscelis adeliae) on Petrel Island, Antarctica

description: 1. In Polar Regions, the extent and dynamics of sea-ice are changing. This affects the ocean productivity which consecutively impacts plankton communities and polar top predators like penguins. Yet, the underlying behavioural and physiological mechanisms remain poorly understood.2. Here we monitored the ecophysiological responses of Adelie penguin (Pygoscelis adeliae) pairs during two seasons of contrasting timing of sea-ice retreat. Beside classical breeding parameters like foraging trip duration, body mass and reproductive success, we also investigated food-related stress (via plasma corticosterone concentration), nutritional state (via metabolite levels) and the use of penguins' habitat (via blood isotopic values). 3. Body mass and reproductive success remained unchanged but foraging trips were shorter when sea-ice retreated earlier. Constant plasma corticosterone concentrations indicated that none of the feeding conditions resulted in a food-related stress. However metabolite levels were lower when sea-ice retreated early, suggesting that the foraging performance and the quality/quantity of food differed. Indeed isotopic ratios indicated that coastal prey like fish contributed more to the penguins' diet when sea-ice retreated prematurely.4. The early sea-ice retreat was related to higher chlorophyll concentrations, known to favour krill recruitment. Paradoxically, this was not associated to a higher krill contribution in the penguins' diet. We propose that a shift in the phytoplankton quality (rather than quantity), affecting krill recruitment, forced penguins to switch to more available prey like coastal fish.5. In some Antarctic regions, sea-ice is retreating earlier and earlier. In the present study, even though the timing of sea-ice retreat and the consecutive ocean productivity differed drastically between the 2 years, Adelie penguins were not severely affected because they were able to adjust their at-sea behaviour and thus maintained their body condition and reproductive success unchanged.6. This suggests that the timing of sea-ice retreat does not represent an important threat to populations of Adelie penguins at least as long as alternative resources are still available and other environmental parameters like winter sea-ice extent are not dramatically altered.
description: Data extracted in the frame of a joint ICSTI/PANGAEA IPY effort, see http://doi.pangaea.de/10.1594/PANGAEA.150150
description: Supplement to: Beaulieu, Michaël; Dervaux, Antoine; Thierry, Anne-Mathilde; Lazin, David; Le Maho, Yvon; Ropert-Coudert, Yan; Spée, Marion; Raclot, Thierry; Ancel, André (2010): When sea-ice clock is ahead of Adelie penguins' clock. Functional Ecology, 24(1), 93-102
DOI: 10.1594/pangaea.783364
title: (Table 2b) Ratios of trace metal to Al concentrations in ODP Hole 161-974C
DOI: 10.1594/pangaea.806578
title: (Table 6) Representative talc and mixed-layer talc-chlorite analyses of ODP Holes 137-504B and 140-504B
DOI: 10.1594/pangaea.626420
title: Soli temperature during expedition LENA 2002, Samoylov Island, S2 location
DOI: 10.1594/pangaea.806502
title: Basic measurements of radiation at station Nauru Island (2002-07)

description: Version 3, 2013-02-01
DOI: 10.1594/pangaea.806747
title: (Table 5) Compositions of amphibole populations at DSDP Holes 81-553A and 81-555
DOI: 10.1594/pangaea.864907
title: Wild bee monitoring in six agriculturally dominated landscapes of Saxony-Anhalt (Germany) in 2011

description: Wild bee species abundance based on combined flight traps (yellow funnels with perspex windows) placed at ecotones between semi-natural habitats and agricultural fields. Design: six agricultural dominated landscapes of 4x4 km with one trap per square km in Saxony-Anhalt (Germany), activity of traps in late spring-early summer (three sampling rounds) and late summer (three sampling rounds).
DOI: 10.1594/pangaea.807086
title: (Table 5) Geochemistry of feldspar at DSDP Hole 81-555

description: Concentrations lower than 0.3% are not considered representative. Analyses 51-56 show core-to-rim compositional variations of a plagiolase phenocryst 250 ?m in diameter.
DOI: 10.1594/pangaea.909411
title: Sand content of ODP Site 178-1096
DOI: 10.1594/pangaea.804205
title: (Table 5a) Chemical composition of interstitial waters from bottom sediments collected in the Middle Caspian Sea at Station Rift29-18
DOI: 10.1594/pangaea.864790
title: Wild bee monitoring in six agriculturally dominated landscapes of Saxony-Anhalt (Germany) in 2010

description: Wild bee species abundance based on combined flight traps (yellow funnels with perspex windows) placed at ecotones between semi-natural habitats and agricultural fields. Design: six agricultural dominated landscapes of 4x4 km with one trap per square km in Saxony-Anhalt (Germany), activity of traps in late spring-early summer (three sampling rounds) and late summer (three sampling rounds).
DOI: 10.1594/pangaea.615987
title: Borehole temperature of Hole LD99-A05-2
DOI: 10.1594/pangaea.804206
title: (Table 5b) Chemical composition of interstitial waters from bottom sediments collected in the Middle Caspian Sea at Station Rift35-2
DOI: 10.1594/pangaea.865038
title: Wild bee monitoring in six agriculturally dominated landscapes of Saxony-Anhalt (Germany) in 2012

description: Wild bee species abundance based on combined flight traps (yellow funnels with perspex windows) placed at ecotones between semi-natural habitats and agricultural fields. Design: six agricultural dominated landscapes of 4x4 km with one trap per square km in Saxony-Anhalt (Germany), activity of traps in late spring-early summer (three sampling rounds) and late summer (three sampling rounds).
DOI: 10.1594/pangaea.806366
title: Continuous meteorological observations at SIMA station Serra da Mesa reservoir in 2013

description: Quality flags: ? = questionable; / = not valid
DOI: 10.1594/pangaea.828963
title: Natural gamma radiation from IODP Hole 339-U1390C

description: Geocode = Depth CSF-A (m)
DOI: 10.1594/pangaea.804207
title: (Table 5c) Chemical composition of interstitial waters from bottom sediments collected in the Middle Caspian Sea at Station Rift35-3
DOI: 10.1594/pangaea.889440
title: Clearance, O2 respiration and NH4 excretion rates of Cerastoderma edule under salinity stress

description: Here we investigate differences on the energetic strategy of thread drifters (3-4mm) and sedentary settlers (9-10mm) of Cerastoderma edule over a wide range of salinities (3, 5, 10, 15, 20, 25, 30 and 35) in a laboratory experiment. Several physiological indicators (clearance, respiration and excretion rates and O:N) were measured during acute (2 days) and acclimated responses (7 days of exposure) for both size classes. Our results revealed a common lethal limit for both developmental stages (Salinity &lt;15) but a larger physiological plasticity of thread drifters than sedentary settlers.
description: Supplement to: Peteiro, Laura Garcia; Woodin, Sarah A; Wethey, David S; Costas-Costas, Damian; Martinez-Casal, Arantxa; Olabarria, Celia; Vázquez, Elsa (2018): Responses to salinity stress in bivalves: Evidence of ontogenetic changes in energetic physiology on Cerastoderma edule. Scientific Reports, 8(1), 8329
DOI: 10.1594/pangaea.909903
title: Radiosonde measurements from station Tamanrasset (2019-11)

description: Start location: Tamanrasset; Distance from radiation site: 10 km
DOI: 10.1594/pangaea.745240
title: (Appendix 1) Temperature, ionic strength, and porewater activity from ODP Leg 168 sites

description: Depth, sediment is given in mbsf. See also Inoue (2000b) dataset: doi:10.1594/PANGAEA.788861.
DOI: 10.1594/pangaea.689929
title: Radiosonde M58_R111 during METEOR cruise M58 on 1981-10-09 11:00h

description: Data processing by Wolfgang Gloeden, Maritime Klimaüberwachung (KU24), Deutscher Wetterdienst, http://www.dwd.de
DOI: 10.1594/pangaea.712762
title: (Table A10) Carbonate, total organic carbon and sulphur content of sediment core POS158/1_0010/2
DOI: 10.1594/pangaea.828944
title: Natural gamma radiation from IODP Hole 339-U1385B

description: Geocode = Depth CSF-A (m)
DOI: 10.1594/pangaea.909774
title: 0-95, 95-244 and 244-378: XRF peak area (Al, Ca, Fe, K, Mn, Si, Sr, Zr) data of sediment core ARA02B/16B-GC from the Arliss Plateau, off the East Siberian margin, western Arctic Ocean
DOI: 10.1594/pangaea.690458
title: Mesozooplankton biomass during Akademik Kovalevsky cruise AK7/1, Part II

description: Mesozooplankton was sampled by open-closing JUDAY net with a 36 cm ring diameter and mesh size of 0.145 mm. The open-closing mechanism used was the Nansen mechanical lock system allowing nets to be vertically towed through standard depths (0-10, 10-25, 25-50, 50-100, 100-200, 200-500 m) and closed at the upper depth level. Depth of tow was evaluated by wire paid out and the angle of wire inclination. The 10-20 ml samples were preserved in 3-4% buffered formaldehyde and processed on return to the laboratory. All of copepods were identified to genus level, other taxanomic groups - to type, class, order and family levels.
DOI: 10.1594/pangaea.807284
title: Radiosonde measurements from station Sapporo (2012-11)
DOI: 10.1594/pangaea.693598
title: Mesozooplankton average length during Akademik Kovalevsky cruise AK65, Part I

description: Mesozooplankton was sampled by open-closing JUDAY net with a 36 cm ring diameter and mesh size of 125 µm. The open-closing mechanism used was the Nansen mechanical lock system allowing nets to be vertically towed through standard depths (0-10, 10-25, 25-50, 50-100, 100-200, 200-300, 300-500 m) and closed at the upper depth level. Depth of tow was evaluated by wire paid out and the angle of wire inclination. The 10-20 ml samples were preserved in 3-4% buffered formaldehyde and processed on return to the laboratory. All of copepods were identified to genus level, other taxanomic groups - to type, class, order and family levels.
DOI: 10.1594/pangaea.711960
title: Pollen profile SLATTEN, Slatten, Sweden

description: The EPD (http://www.europeanpollendatabase.net) accepted species name is given in the parameter comment. This dataset was archived on 2010-05-11 from the EPD database.
DOI: 10.1594/pangaea.777550
title: (Table 2) Grain size composition of Pacific deep sea red clays between 17 and 23°N
DOI: 10.1594/pangaea.909688
title: Closed porosity tomography measurements of the Lock-In firn and ice core (80-112 m depth)

description: Porosity data obtained with tomographic imagery at the Institute for Snow and Avalanche Research SLF, Davos, Switzerland
DOI: 10.1594/pangaea.693604
title: Mesozooplankton average length during Akademik Kovalevsky cruise AK90, Part II

description: Mesozooplankton was sampled by open-closing JUDAY net with a 36 cm ring diameter and mesh size of 125 µm. The open-closing mechanism used was the Nansen mechanical lock system allowing nets to be vertically towed through standard depths (0-10, 10-25, 25-50, 50-100, 100-200, 200-300, 300-500 m) and closed at the upper depth level. Depth of tow was evaluated by wire paid out and the angle of wire inclination. The 10-20 ml samples were preserved in 3-4% buffered formaldehyde and processed on return to the laboratory. All of copepods were identified to genus level, other taxanomic groups - to type, class, order and family levels.
DOI: 10.1594/pangaea.772288
title: (Table III.4.2a) Grain size composition of surface layer sediments from the Liberian shelf and the Congo River mouth area
DOI: 10.1594/pangaea.832051
title: (Table TS05) Measured or extrapolated ages of core tops older than 5000 years of sediment cores from the Agulhas current
DOI: 10.1594/pangaea.739270
title: Pollen profile GONDO, Gondo Alpjen, Switzerland

description: The EPD (http://www.europeanpollendatabase.net) accepted species name is given in the parameter comment. This dataset was archived on 2010-05-11 from the EPD database.
DOI: 10.1594/pangaea.822841
title: Meteorological measurements in the upper air at station Friedrichshafen, 1919-04-25 to 1920-08-31, ERA-CLIM ID 5674

description: Altitude = Height above sea-level
DOI: 10.1594/pangaea.845230
title: Station list and links to master tracks in different resolutions of HEINCKE cruise HE362, Bremerhaven - Bremerhaven, 2011-08-02 - 2011-08-14
DOI: 10.1594/pangaea.746714
title: Physical properties of snowpit NYA_S1
DOI: 10.1594/pangaea.828900
title: Pass-through measurements of magnetic susceptibility from IODP Hole 339-U1387A

description: Geocode = Depth CSF-A (m)
DOI: 10.1594/pangaea.759061
title: (Table 5) Composition of major oxides of various crystals in tephra layers at ODP Site 121-758
DOI: 10.1594/pangaea.912341
title: Pore water sulfate and chloride concentrations of MeBo sediment core GMMB02 collected in the area of Pockmark A
DOI: 10.1594/pangaea.688666
title: Mesozooplankton abundance and biomass in surface waters of the Aegean Sea in spring 1997. Station MARCH-1997-GN36199704601MSB07wp2

description: A Stempel pipette has been used for subsamples in taxonomic analysis of zooplankton. Taxonomic identification has been done at the P.P. Shirshov Institute of Oceanography by I. Siokou-Frangou and E. Christou with use of relevant taxonomic literature.Mesozooplankton biomass was estimated as dry-weight (mg/m**3) according to M. Omori and T. Ikeda (Methods in Marine Zooplankton Ecology. New York, John Wiley & Sons. 1984. 311 p.). A Folsom splitter has been used for biomass and abundance estimations in 4% formaldehyde buffered sub-samples.
DOI: 10.1594/pangaea.692363
title: Concentrations of chlorophyll-alpha in sea water from the euphotic zone at Station SEPT-94-GN3619940280300590 in the Aegean Sea

description: Samples from 2 l of sea water were filtered through polycarbonate Millipore. The filters were kept deep frozen and analyzed according to Holm-Hansen et al. (Holm-Hansen, O., Lorenzen, C.J., Holmes, R.W., Strickland, J.D.H. 1965. Fluorometric determination of chlorophyll. Journal du Conseil Permanent International Pour l'Exploration de la Mer 30, 3-15).
DOI: 10.1594/pangaea.693625
title: Mesozooplankton average length during Professor Vodyanitskiy cruise PV12, Part IV

description: Mesozooplankton was sampled by open-closing JUDAY net with a 36 cm ring diameter and mesh size of 125 µm. The open-closing mechanism used was the Nansen mechanical lock system allowing nets to be vertically towed through standard depths (0-10, 10-25, 25-50, 50-100, 100-200, 200-300, 300-500 m) and closed at the upper depth level. Depth of tow was evaluated by wire paid out and the angle of wire inclination. The 10-20 ml samples were preserved in 3-4% buffered formaldehyde and processed on return to the laboratory. All of copepods were identified to genus level, other taxonomic groups - to type, class, order and family levels.
DOI: 10.1594/pangaea.692387
title: Concentrations of chlorophyll-alpha in sea water from the euphotic zone at Station DEC94-JAN95-GN3619940280400590 in the Aegean Sea

description: Samples from 2 l of sea water were filtered through polycarbonate Millipore. The filters were kept deep frozen and analyzed according to Holm-Hansen et al. (Holm-Hansen, O., Lorenzen, C.J., Holmes, R.W., Strickland, J.D.H. 1965. Fluorometric determination of chlorophyll. Journal du Conseil Permanent International Pour l'Exploration de la Mer 30, 3-15).
DOI: 10.1594/pangaea.692388
title: Concentrations of chlorophyll-alpha in sea water from the euphotic zone at Station DEC94-JAN95-GN3619940280400750 in the Aegean Sea

description: Samples from 2 l of sea water were filtered through polycarbonate Millipore. The filters were kept deep frozen and analyzed according to Holm-Hansen et al. (Holm-Hansen, O., Lorenzen, C.J., Holmes, R.W., Strickland, J.D.H. 1965. Fluorometric determination of chlorophyll. Journal du Conseil Permanent International Pour l'Exploration de la Mer 30, 3-15).
DOI: 10.1594/pangaea.692093
title: Age determination on sediment core GIK12519-2
DOI: 10.1594/pangaea.829682
title: Station list and links to master tracks in different resolutions of HEINCKE cruise HE411
DOI: 10.1594/pangaea.915476
title: Electrical conductivity, porosity and density of sediment core GeoB18514-2
DOI: 10.1594/pangaea.872280
title: Links to master tracks in different resolutions from POLAR 2 flight EPICA_I_13
DOI: 10.1594/pangaea.808383
title: (Electronic annex 2) Mercury species concentration in seawater samples near Casey Station, Antarctica
DOI: 10.1594/pangaea.692268
title: Mesozooplankton biomass during Professor Vodyanitskiy cruise PV12, Part III

description: Mesozooplankton was sampled by open-closing JUDAY net with a 36 cm ring diameter and mesh size of 125 µm. The open-closing mechanism used was the Nansen mechanical lock system allowing nets to be vertically towed through standard depths (0-10, 10-25, 25-50, 50-100, 100-200, 200-300, 300-500 m) and closed at the upper depth level. Depth of tow was evaluated by wire paid out and the angle of wire inclination. The 10-20 ml samples were preserved in 3-4% buffered formaldehyde and processed on return to the laboratory. All of copepods were identified to genus level, other taxonomic groups - to type, class, order and family levels.
DOI: 10.1594/pangaea.688694
title: Stable carbon and oxygen isotope composition of Recent, Tertiary and Cretaceous foraminifera (Table III)

description: Oxygen isotope analyses of Tertiary and Cretaceous planktic foraminifera indicate that species have been stratified with respect to depth in the water column at least since Albian time. There is a relationship between morphology and depth habitat. Species with globigerine morphology have consistently occupied shallower depths than have species with globorotalid morphology. Biserially arranged species occupied both shallow and deep levels in the water column. On the average, it appears that ancient species with shallow habitats have been more susceptible to dissolution and have been preserved less well than species dwelling in deeper habitats. This relationship is similar to that observed for Recent planktic foraminifera. Comparison of carbon isotope ratios of adult and juvenile forms indicates that either the source of the carbon found in the shell or the carbon isotopic fractionations which occur during calcite secretion change during the development of individual foraminifera. The carbon isotopic ratios do not provide a reliable means for reconstructing the depth habitats of ancient species. Temperature-depth profiles for tropical Tertiary oceans have been reconstructed from the isotopic temperatures of planktic and benthic foraminifera. The vertical thermal structure of Oligocene oceans resembled that of modern oceans most closely. Those of Paleocene and Maastrichtian times differed most from that of modern oceans.
description: Supplement to: Douglas, Robert G; Savin, Samuel M (1978): Oxygen isotopic evidence for the depth stratification of Tertiary and Cretaceous planktic foraminifera. Marine Micropaleontology, 3(2), 175-196
DOI: 10.1594/pangaea.708404
title: (Table 1) Major element contents in host clinopyroxenes from ODP Hole 157-956B
DOI: 10.1594/pangaea.720818
title: Documentation of sediment core GIK23298-2
DOI: 10.1594/pangaea.807812
title: Hydrochemistry measured on water bottle samples during Håkon Mosby cruise CARDEEP4/94
DOI: 10.1594/pangaea.828893
title: Pass-through measurements of magnetic susceptibility from IODP Hole 339-U1385B

description: Geocode = Depth CSF-A (m)
DOI: 10.1594/pangaea.712760
title: (Table A10) Carbonate, total organic carbon and sulphur content of sediment core POS158/1_0008/1
DOI: 10.1594/pangaea.775814
title: (Table T4) Chemical composition of minerals from ODP Holes 206-1256C and 206-1256D

description: Sediment depth is given in mbsf. Chemical formulas were calculated for phyllosilicates based on a layer charge of 22 (10 oxygens and 2 hydroxyls).
DOI: 10.1594/pangaea.915488
title: Electrical conductivity, porosity and density of sediment core GeoB18551-2
DOI: 10.1594/pangaea.712775
title: (Table A10) Carbonate, total organic carbon and sulphur content of sediment core POS158/1_0023/1
DOI: 10.1594/pangaea.915489
title: Electrical conductivity, porosity and density of sediment core GeoB18552-1
DOI: 10.1594/pangaea.705508
title: (Table 2) Total number of benthic foraminifera below the K/T boundary in DSDP Hole 62-465A