cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.940933
title: Amino acids and hexosamines in water and pore water samples from different oceanic areas sampled between 2013 and 2016

description: These water and pore water samples were collected in different oceanic areas between 2013 and 2016. The samples were compiled from previous studies and used for statistical analyses in order to better understand particle dynamics and organic matter cycling in the ocean and to test and refine amino acid (AA) and hexosamine (HA) based biogeochemical indicators. Dissolved organic carbon (DOC) concentrations and total dissolved nitrogen (TDN) concentrations were determined with a POC-VCSH analyzer (Shimadzu) after removal of inorganic carbon by 2M HCl. Stable nitrogen and oxygen isotopes of nitrate (δ15N-NO3, δ18O-NO3) were analysed by the denitrifier method with a Delta Plus XP mass spectrometer. AA and HA contents and their individual monomers were analysed by liquid chromatography using a Biochrom 30 amino acid analyser after acid hydrolysis of filtered sea or pore water. Contents of AA and HA are presented in µmol/L and µg/L. AAC, AAN, HAC, HAN are presented in µg/L and as percentages of DOC (AAC/C, HAC/C) or TDN (AAN/N, HAN/N). AA and HA monomers are presented in Mol% and comprise aspartic acid (ASP), glutamic acid (Glu), threonine (Thr), serine (Ser), glycine (Gly), alanine (Ala), valine (Val), methionine (Met), isoleucine (Ile), leucine (Leu), tyrosine (Tyr), phenylalanine (Phe), β-Alanine (β-Ala), γ-aminobutyric acid (γ-Aba), histidine (His), ornithine (Orn), lysine (Lys) and arginine (Arg), glucosamine (GlcN) and galactosamine (GalN). Cysteic acid (CYA), taurine (TAU), methionine sulfoximine (MSO) and tryptophane (TRP) were determined only in the more recent samples. Data gaps indicate that measurements were not carried out or that they were not stored in the older data sets. The RI was calculated according to Jennerjahn and Ittekkot (1997; https://archimer.ifremer.fr/doc/00093/20403/) and the DI after Dauwe et al. (1999; doi:10.4319/lo.1999.44.7.1809). Definitions of biogeochemical indicators SDI, RTI, ox/anox and a detailed description of the methods can be found in Gaye et al. (2022; doi:org/10.5194/bg-19-807-2022).
DOI: 10.22002/f4nnb-69061
title: NLBi Fixed 293T

description: wild type, 293T, fixed
description: <strong>Tilt Series Date:</strong> 2014-07-03</p>
<strong>Data Taken By:</strong> Luiza Mendonca</p>
<strong>Species / Specimen:</strong> HIV and deltaNef</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -8.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> fixed w/ 1% formaldehyde</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lmm2014-07-03-3/rawdata/</p>L025_3_NLBi_293T_fixed0003.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        L025_3_NLBi_293T_fixed0003_full.rec,  Reconstruction (Pixel Size 2.0 nm), 445.4 MB  
        
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DOI: 10.1594/pangaea.786248
title: Stable isotopes measured on benthic foraminifers of sediment core SO201-2-85

description: Investigator: L. Max
DOI: 10.1594/pangaea.848848
title: Stable isotopes, Mg/Ca ratios and sea surface temperatures on planktonic and benthic foraminifera of sediment core M77/2_059-1

description: Parameter Alkenone, C36 was set by an error. Here Alkenone, C37:2+C37:4 was measured, parameter changed on 2017-09-27 based on pers. com. with R. Schneider
DOI: 10.1594/pangaea.967432
title: Dissolved inorganic nutrient concentration of Lena River water from 20.04.2018 (#1) to 11.09.2019 (#201)

description: We collected water samples from the river surface in the center of the Olenekskaya Channel near Samoylov Island using a pre-rinsed HDPE 1 L bottle. During the open water period (June to October), water was sampled from a small boat, and during ice-covered period (November to May), through a hole drilled through the river ice. Some samples during the river ice break-up (between May and June) as well as some samples during the ice freeze-up in October were taken from the shore due to the inaccessibility of a more centered location on the river channel. Samples for dissolved inorganic nutrient analysis (silicate, ammonium, phosphate, nitrite, and nitrate) were filtered through a 0.45 μm cellulose acetate filter, which had been rinsed with 20 mL sample water. Dissolved inorganic nutrients for samples #001 - #201 (20 Apr. 2018 to 11 Sept. 2019) were measured at the Otto Schmidt Laborator in St. Petersburg, Russia. Nutrient concentrations were analyzed on an automated continuous flow system (San+, SKALAR, Netherlands) with standard colorimetric techniques (Aminot et al. 2009).
DOI: 10.1594/pangaea.786283
title: Stable isotopes measured on benthic foraminifers of sediment core SO201-2-85
DOI: 10.1594/pangaea.756436
title: Stable oxygen ratios of epibenthic foraminifer Cibicidoides wuellerstorfi from sediment core GeoB9526-5, 355 - 980 cm

description: see further details for stable isotope ratios from the top of profile (0 - 350 cm)
DOI: 10.1594/pangaea.864051
title: Stable oxygen isotope ratios of Neogloboquadrina pachyderma s from sediment core MD99-2236
DOI: 10.22002/hvt4a-cvx98
title: E.coli   "strain 2748"

description: UU 2748 tsr-E248Lkinase off
description: <strong>Tilt Series Date:</strong> 2012-04-04</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> RP 437</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> John S. Parkinson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in TB at 30 degrees, lysed with Penicillin for one hour</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2012-04-04-10/rawdata/</p>UU27480002.mrc,  Tilt Series (Pixel Size 0.644 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2012-04-04-10/rawdata/UU27480002.mrc"
        > <i class="download icon"></i> Download </a></p>

        UU27480002_part128_58.rec,  Reconstruction (Pixel Size 1.288 nm), 516.1 MB  
        
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DOI: 10.1594/pangaea.756415
title: Age determination of sediment core GeoB9526-5
DOI: 10.1594/pangaea.864050
title: Stable oxygen isotope ratios of Elphidium excavatum from sediment core MD99-2236
DOI: 10.1594/pangaea.733068
title: (Fig. 6) Planktonic foraminifer stable isotope records of sediment core MD99-2339

description: measured on a Finnigan MAT 251 Leibniz lab Kiel and on a Finnigan MAT 251 or 252 at MARUM Bremen
DOI: 10.1594/pangaea.465027
title: (Fig. 2) Stable oxygen and carbon isotopes of Cibicides lobatulus from sediment core MD99-2339
DOI: 10.1594/pangaea.786257
title: Opal of sediment core SO201-2-85
DOI: 10.1594/pangaea.837182
title: Stable oxygen isotope record of Globigerinoides ruber from sediment core MD06-3075
DOI: 10.22002/hx7bk-fpc94
title: Agro delta_rem 28C liq

description: apr-12-2014, confirmed virb2 by western
description: <strong>Tilt Series Date:</strong> 2014-04-12</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> autoPatch</p>
<strong>Collaborators and Roles:</strong> clay fuqua</p>
<strong>Purification / Growth Conditions / Treatment:</strong> AB media, +acetosyringone ~24 hrs</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-04-12-2/rawdata/</p>agro_rem_28liq0002.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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        agro_rem_28liq0002.rec,  Reconstruction (Pixel Size 1.92 nm), 1.1 GB  
        
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DOI: 10.22002/mzxjg-nj451
title: H.hepaticus

description: Helicobacter hepaticus cell poles
description: <strong>Tilt Series Date:</strong> 2013-04-06</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Helicobacter hepaticus</p>
<strong>Strain:</strong> ATCC 51449</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 1°, constant angular increment, dosage: 165.0 eV/Å²,  defocus: -10.0 μm,  magnification: 41000x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> grown in the Mazmanian lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in the Mazmanian lab</p>
  aba2013-04-06-9_slicer4941.jpg: 2 layer peptidoglycan
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-04-06-9/rawdata/</p>hepaticus41mag0004.mrc,  Tilt Series (Pixel Size 0.28 nm), 3.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-04-06-9/rawdata/hepaticus41mag0004.mrc"
        > <i class="download icon"></i> Download </a></p>

        hepaticus41mag0004_part133_8.rec,  Reconstruction (Pixel Size 1.12 nm), 706.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-04-06-9/3dimage_26965/hepaticus41mag0004_part133_8.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.qy7u4e
title: Occurrence Download

description: A dataset containing 6246 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Symplocos sumuntia"
 ]
}

 The dataset includes 6246 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002125-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.756409
title: (Fig. 6a) Accumulation rates, carbon and carbonate content of sediment profile GeoB9526
DOI: 10.22002/0cfjn-50j13
title: B. subtilis minicell lysate

description: B subtilis strain DK 720 minicell lysate
description: <strong>Tilt Series Date:</strong> 2013-09-05</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -8.0 μm,  magnification: 34000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Dan Kearns</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Minicell isolation and Lysozyme lysis</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-05-27/rawdata/</p>Bacilluslysemini0030.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-05-27/rawdata/Bacilluslysemini0030.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bacilluslysemini0030_part121_9.rec,  Reconstruction (Pixel Size 1.28 nm), 712.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.266634
title: Sea surface temperatures reconstructed from sediment core GIK35003-4
DOI: 10.22002/bhj5y-zn847
title: E. coli (FB76)

description: Contains MreB-mCherry sandwich fusion as sole source of MreB from WT promoter.
description: <strong>Tilt Series Date:</strong> 2012-05-07</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: None μm,  magnification: 23000x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> Gift from Piet de Boer</p>
<strong>Purification / Growth Conditions / Treatment:</strong> LB, 30 Degrees Celsius, OD600 ~ 0.6</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2012-05-07-15/rawdata/</p>20120507_FB76_M12.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2012-05-07-15/rawdata/20120507_FB76_M12.mrc"
        > <i class="download icon"></i> Download </a></p>

        20120507_FB76_M12_full.rec,  Reconstruction (Pixel Size 1.9 nm), 825.8 MB  
        
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DOI: 10.1594/pangaea.218138
title: (Appendix 6) Stable oxygen isotope ratios of benthic foraminifera from sediment core LV28-42-4

description: Measured on 2-3 species of the endobenthic foraminiferal species Uvigerina auberiana and Uvigerina aktiaensis (Uvigerina peregrina of authors) from the 250-500 um size fraction.
DOI: 10.1594/pangaea.756435
title: Sea surface temperature reconstruction based on the Mg/Ca ratio of planktonic foraminifera Globigerinoides ruber pink in sediment core GeoB9508-5
DOI: 10.1594/pangaea.909094
title: Dissolved Organic Matter and Trace Metal Composition in Rivers Draining Degraded Tropical Peatlands in West Kalimantan, Indonesia

description: This dataset comprises water samples collected in the surrounding of Pontianak (0.09°N, 109.24°E) on the island of Borneo. Two sampling campaigns were conducted in June 2013 (drier period) and January 2014 (wetter period). Using a boat, samples were collected in the center of the river, from the origin of the Ambawang river (BR, black river sites) to its downstream confluence with the Landak and Kapuas KecilKecil (WR, white river sites). White river samples collected upstream of the confluence with the white river (WRu, white river upstream). Drainage canals (DC) flowing into the black river were also sampled during the second sampling campaign. In January 2014, a rain collector was installed on the roof of the Pontianak's meteorological station to collect rain samples for lead isotopic analysis.
DOI: 10.1594/pangaea.261313
title: Foraminifera, sedimentological parameters and sea surface temperature and salinity calculated on core SO82_5-2
DOI: 10.1594/pangaea.208132
title: Stable oxygen isotopes (δ¹⁸O) of sediment core MD97-2120
DOI: 10.1594/pangaea.759279
title: (Table A4) Stable oxygen isotope data obtained on Globigerinoides sacculifer in sediment core SO164-17-2
DOI: 10.22002/849yx-hdh97
title: Protochlamydia amoebophila Cryosections

description: Cryosections of infected amoeba cells
description: <strong>Tilt Series Date:</strong> 2012-03-30</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Protochlamydia amoebophila</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: °, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Matthias Horn</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cryosections</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2012-03-30-24/rawdata/</p>10012012_CS_S6_y0042.st,  Tilt Series (Pixel Size 1.23 nm), 416.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10012012_CS_S6_y0042.rec,  Reconstruction (Pixel Size 1.23 nm), 154.6 MB  
        
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DOI: 10.1594/pangaea.201812
title: Stable isotope analysis of foraminifera from sediment core SO82_5-2
DOI: 10.1594/pangaea.465028
title: (Fig. 2) Stable oxygen and carbon isotopes of Cibicidoides pachyderma from sediment core MD99-2339

description: Datasets update: 2019-07-11, isotope measuerement column headings were inverted.
DOI: 10.1594/pangaea.777692
title: 6) SST, seawater δ¹⁸O, IRD, planktic and benthic foraminiferal stable isotope data from core ODP 980: revised chronology for the Last Interglacial (period 135-110 ka)

description: Age: Correlation to Greenland and Antarctic ice cores.
DOI: 10.1594/pangaea.854419
title: Registry of samples and environmental context from the Ocean Sampling Day 2014

description: The Ocean Sampling Day (OSD) is a simultaneous sampling campaign of the world's oceans which took place (for the first time) on the summer solstice (June 21st) in the year 2014. These cumulative samples, related in time, space and environmental parameters, provide insights into fundamental rules describing microbial diversity and function and contribute to the blue economy through the identification of novel, ocean-derived biotechnologies. We see OSD data as a reference data set for generations of experiments to follow in the coming decade. The present data set includes a description of each sample collected during the Ocean Sampling Day 2014 and provides contextual environmental data measured concurrently with the collection of water samples for genomic analyses.
DOI: 10.1594/pangaea.856560
title: Planktonic foraminiferal oxygen isotopes and trace element data of sediment core HU91-045-093
DOI: 10.1594/pangaea.842197
title: Methodological context of all samples from the Tara Oceans Expedition (2009-2013)

description: The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set is a registry of all samples collected during the Tara Oceans Expedition (2009-2013). The registry provides details about the sampling location and methodology of each sample. Uniform resource locators (URLs) offer direct links to additional contextual environmental data published at PANGAEA, and to the corresponding nucleotides data published at the European Nucleotides Archive (EBI-ENA).
DOI: 10.22002/1f79q-4h398
title: HUVECs 24h PI pNLBglI

description: Whole cells were grown on Au finder grids and infected with pNLGFPBglI. Sample frozen 24h post infection
description: <strong>Tilt Series Date:</strong> 2013-05-10</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HUVECs</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19000x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Whole cells were grown on Au finder grids and infected with pNLGFPBglI. Sample frozen 24h post infection</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-05-10-18/rawdata/</p>C161-4ATB0018.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-05-10-18/rawdata/C161-4ATB0018.mrc"
        > <i class="download icon"></i> Download </a></p>

        C161-4ATB0018_full.rec,  Reconstruction (Pixel Size 2.4 nm), 516.7 MB  
        
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DOI: 10.1594/pangaea.465030
title: (Fig. 2) Stable oxygen and carbon isotopes of Cibicidoides wuellerstorfi from sediment core MD99-2339
DOI: 10.1594/pangaea.700135
title: Stable isotope record of Cibicidoides wuellerstorfi of sediment core MD06-2990
DOI: 10.1594/pangaea.835176
title: δ¹⁸O and δ¹³C of Cibicidoides wuellerstorfi from sediment core WIND28K
DOI: 10.1594/pangaea.834395
title: (Table DR1) UK'37 and alkenone temperature data derived from sediment core SO201-2-85KL