cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/0hac2-dge18
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</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> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-72/rawdata/</p>JV9082_201808290037.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-72/rawdata/JV9082_201808290037.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290037_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-72/3dimage_96479/JV9082_201808290037_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.959510
title: Uranium-thorium dating of Atlantic cold-water corals from the last 32,000 years

description: Uranium-thorium dating offers the possibility of absolute age determination of cold-water corals (CWCs). We present here the complementary dataset to "Radiocarbon dating of Atlantic cold-water corals over the last 32.000 years". It contains 230Th/U ages obtained on CWCs from various locations in the central and east Atlantic Ocean, as well as the Alboran Sea. It also includes an update of previously published data, necessitated by a recently discovered "ghost signal" (Kerber et al., 2023). U and Th were extracted according to the method of Wefing et al. (2017). The high precision isotopic measurements were performed on a multi-collector inductively coupled plasma mass spectrometer (MC-ICP-MS, Thermo Fisher Neptune Plus) at the Institute of Environmental Physics, Heidelberg University, Germany. For age calculations the half-lives of 234U and 230Th published in (Cheng et al., 2013) were used. The mass spectrometry setup and data treatment follows the methods recently updated in great detail by Kerber et al. (2023).
DOI: 10.1594/pangaea.959515
title: Radiocarbon dating of Atlantic cold-water corals over the last 32,000 years

description: The radiocarbon analysis of uranium-thorium-dated cold-water corals (CWCs) provides an excellent opportunity for qualitative reconstruction of past ocean circulation and water mass aging. While mid-depth water mass aging has been studied in the Atlantic Ocean, the evolution of the thermocline, tightly coupled to the atmosphere, is still largely unknown. Here we present a combined 14C and 230Th/U age record obtained from thermocline dwelling CWCs with partially centennial resolution over the last 32 ka at various locations in the central and east Atlantic Ocean (Azores Front, Mauritania, Angola), as well as in the Alboran Sea. Preparation for radiocarbon dating took place at the Institute of Environmental Physics, Heidelberg University, Germany (Therre et al., 2021). The samples were measured on an accelerator mass spectrometer (MICADAS) at the Curt-Engelhorn Center for Archaeometry in Mannheim, Germany (Kromer et al., 2013, Synal et al., 2007).
DOI: 10.22002/4xp1y-f2n94
title: P_aeruginosa_PA14_DfliF_Krios

description: Raw data files of P_aeruginosa_PA14_DfliF_Krios
description: <strong>Tilt Series Date:</strong> 2018-09-29</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (50.0°, -50.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -9.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Collaborators and Roles:</strong> I (mohammed) obtained the cells from Shannon Park (Dianne Newman lab). The cells are available in their library of Pseudomonas aeruginosa PA14.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I inoculated one colony from an LB agar plate and grew the cells overnight in LB with 100 ug/ml of Gentamycin. Then I concentrated the cells three times and mixed them with gold nanoparticles and added 3 ul on to thick carbon R2 grids and blotted them and plunge froze them (force either 6 or 3, time either 3 or 2 seconds respectively, drain time 1 second).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-13/rawdata/</p>Pseudomonas_DfliF19.mrc,  Tilt Series (Pixel Size 0.53 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-13/rawdata/Pseudomonas_DfliF19.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudomonas_DfliF19_part58_4.rec,  Reconstruction (Pixel Size 2.12 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-13/3dimage_97150/Pseudomonas_DfliF19_part58_4.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.1594/pangaea.915099
title: Uranium-series (calculated) ages obtained from cold-water coral fragments collected from coral mounds of the Belgica coral mound province

description: Table 4. Uranium-series (calculated) ages obtained from cold-water coral fragments collected from coral mounds of the Belgica coral mound province (PO: Poseidon, LH: Lion's Head, GA: Galway, PX: Pollux; for position see Fig. 1B). Supplemented are 232Th concentrations and decay corrected 234U/238U activity ratios (δ234U(i); calculated from the given ages and with λ234U: 2.8263×10−6 yr−1). Note: 22 ages are reliable (R) with δ234U(i) values of 146.8±10‰ (modern seawater; Andersen et al. 2010); 11 ages ranging between 200 and 650 ka BP are unreliable and only presented in the Supplementary Material.
DOI: 10.1594/pangaea.940734
title: Grain size analysis of sediment core MD13-3455G from the East Melilla Coral Province, Mediterranean Sea
DOI: 10.1594/pangaea.940736
title: Grain size analysis of sediment core MD13-3459G from the East Melilla Coral Province, Mediterranean Sea
DOI: 10.1594/pangaea.940737
title: Grain size analysis of sediment core MD13-3462G from the East Melilla Coral Province, Mediterranean Sea
DOI: 10.1594/pangaea.940739
title: XRF analysis of sediment core MD13-3455G from the East Melilla Coral Province, Mediterranean Sea
DOI: 10.22002/8d6w4-n2564
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 10 nm . gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-435/rawdata/</p>Hpylori_DFliF_FISE_440.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-435/rawdata/Hpylori_DFliF_FISE_440.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_440_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-435/3dimage_114330/Hpylori_DFliF_FISE_440_full.rec"
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DOI: 10.1594/pangaea.940741
title: XRF analysis of sediment core MD13-3459G from the East Melilla Coral Province, Mediterranean Sea
DOI: 10.1594/pangaea.940742
title: XRF analysis of sediment core MD13-3462G from the East Melilla Coral Province, Mediterranean Sea
DOI: 10.1594/pangaea.777299
title: Water column measurements of halocarbons during POSEIDON cruise POS399 in June 2010
DOI: 10.1594/pangaea.925801
title: Reproductive features of the deep-sea octocorals Dentomuricea aff. meteor and Viminella flagellum in the Azores

description: Deep-water octocorals form rich communities known as "coral gardens", considered priority habitats for protection. Despite their importance as habitat-builders, our knowledge on their reproductive biology is rarely available. The objective of this study was to collect data on reproductive parameters of two common habitat-forming octocorals in depths between 200 and 600: Dentomuricea aff. meteor and Viminella flagellum. Specimens were collected during 2010 and 2011 as by-catch from deep-sea long-line fisheries and scientific cruises and were histologically processed. Both species were found to be gonochoric, broadcast spawning with continuous gamete presence and overlapping reproductive cycles. The produced data include gamete presence, gamete size and polyp fecundity across different months during the study period.
DOI: 10.1594/pangaea.974424
title: FerryBox-integrated membrane-based pCO2, temperature, salinity, oxygen, chlorophyll, turbidity and pH measurements of BU-C-2107 during RV Burchana cruise

description: The submitted data were collected with a FerryBox-Device on RV Burchana in the transitional and coastal waters of Lower Saxony, Germany. It contains data for temperature, salinity, pH, chlorophyll, oxygen, turbidity and carbon dioxide partial pressure (pCO2) at a water depth of approximately 1.3 m. Within the Carbostore project, totally 8 measurement campaigns were carried out in the years 2021 to 2023. The data is reprocessed and related to a 60 s period. In order to obtain a complete (but rough) overview of the pCO2 situation in this area, values outside the calibration limits (200-1000 µatm) were retained. Dissolved oxygen measurements were corrected by temperature and salinity. The sensors are regularly calibrated, maintained and replaced if necessary. The files are named according to the project, the year and the month of the campaign.
description: The samples for TA/DIC etc. are only taken at the points with the marked sample ID. Samples were therefore not always taken right at the beginning. The remaining data are FerryBox data only and not points where samples were collected.
DOI: 10.22002/p6rx0-b5694
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</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> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-336/rawdata/</p>JV9082_20180901a0110.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-336/rawdata/JV9082_20180901a0110.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_20180901a0110_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-336/3dimage_97043/JV9082_20180901a0110_full.rec"
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DOI: 10.1594/pangaea.974425
title: FerryBox-integrated membrane-based pCO2, temperature, salinity, oxygen, chlorophyll, turbidity and pH measurements of BU-C-2110 during RV Burchana cruise

description: The submitted data were collected with a FerryBox-Device on RV Burchana in the transitional and coastal waters of Lower Saxony, Germany. It contains data for temperature, salinity, pH, chlorophyll, oxygen, turbidity and carbon dioxide partial pressure (pCO2) at a water depth of approximately 1.3 m. Within the Carbostore project, totally 8 measurement campaigns were carried out in the years 2021 to 2023. The data is reprocessed and related to a 60 s period. In order to obtain a complete (but rough) overview of the pCO2 situation in this area, values outside the calibration limits (200-1000 µatm) were retained. Dissolved oxygen measurements were corrected by temperature and salinity. The sensors are regularly calibrated, maintained and replaced if necessary. The files are named according to the project, the year and the month of the campaign.
description: The samples for TA/DIC etc. are only taken at the points with the marked sample ID. Samples were therefore not always taken right at the beginning. The remaining data are FerryBox data only and not points where samples were collected.
DOI: 10.1594/pangaea.974426
title: FerryBox-integrated membrane-based pCO2, temperature, salinity, oxygen, chlorophyll, turbidity and pH measurements of BU-C-2203 during RV Burchana cruise

description: The submitted data were collected with a FerryBox-Device on RV Burchana in the transitional and coastal waters of Lower Saxony, Germany. It contains data for temperature, salinity, pH, chlorophyll, oxygen, turbidity and carbon dioxide partial pressure (pCO2) at a water depth of approximately 1.3 m. Within the Carbostore project, totally 8 measurement campaigns were carried out in the years 2021 to 2023. The data is reprocessed and related to a 60 s period. In order to obtain a complete (but rough) overview of the pCO2 situation in this area, values outside the calibration limits (200-1000 µatm) were retained. Dissolved oxygen measurements were corrected by temperature and salinity. The sensors are regularly calibrated, maintained and replaced if necessary. The files are named according to the project, the year and the month of the campaign.
description: The samples for TA/DIC etc. are only taken at the points with the marked sample ID. Samples were therefore not always taken right at the beginning. The remaining data are FerryBox data only and not points where samples were collected.
DOI: 10.1594/pangaea.974428
title: FerryBox-integrated membrane-based pCO2, temperature, salinity, oxygen, chlorophyll, turbidity and pH measurements of BU-C-2207 during RV Burchana cruise

description: The submitted data were collected with a FerryBox-Device on RV Burchana in the transitional and coastal waters of Lower Saxony, Germany. It contains data for temperature, salinity, pH, chlorophyll, oxygen, turbidity and carbon dioxide partial pressure (pCO2) at a water depth of approximately 1.3 m. Within the Carbostore project, totally 8 measurement campaigns were carried out in the years 2021 to 2023. The data is reprocessed and related to a 60 s period. In order to obtain a complete (but rough) overview of the pCO2 situation in this area, values outside the calibration limits (200-1000 µatm) were retained. Dissolved oxygen measurements were corrected by temperature and salinity. The sensors are regularly calibrated, maintained and replaced if necessary. The files are named according to the project, the year and the month of the campaign.
description: The samples for TA/DIC etc. are only taken at the points with the marked sample ID. Samples were therefore not always taken right at the beginning. The remaining data are FerryBox data only and not points where samples were collected.
DOI: 10.22002/0sg0s-2hk63
title: JV9082_K3_janelia

description: JV9082:DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2019-12-04</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: -3.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Data collected at Janelia Krios (K3 camera). Mag: 26000, pixel size: 2.61A. Defocus range -2 to -4 um.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-04-39/rawdata/</p>9082_Box1_No4_S77.mrc,  Tilt Series (Pixel Size 0.261 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        9082_Box1_No4_S77_full.rec,  Reconstruction (Pixel Size 1.044 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.s2h6r2
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Baileychromis centropomoides, Barboides gracilis, Barbopsis devecchii, Barbus hondeensis, Enteromius manicensis, Barbus kamaia, Enteromius motebensis, Barbus microbarbis, Labeobarbus microbarbis, Barbus microterolepis, Labeobarbus microterolepis, Barbus myersi, Enteromius radiatus, Barbus paucisquamatus, Labeobarbus paucisquamatus, Barbus tetraspilus, Barilius shariensis, Raiamas shariensis, Bathyaethiops breuseghemi, Bathyaethiops caudomaculatus, Bathyaethiops greeni, Bathybagrus grandis, Bathybagrus graueri, Bathybagrus platycephalus, Bathybagrus sianenna, Bathybagrus stappersii, Bathybagrus tetranema, Bathybates fasciatus, Bathybates ferox, Bathybates graueri, Bathybates hornii, Bathybates leo, Bathybates minor, Bathybates vittatus, Bathyclarias atribranchus, Bathyclarias euryodon, Bathyclarias filicibarbis, Bathyclarias foveolatus, Bathyclarias longibarbis, Bathyclarias nyasensis, Bathyclarias rotundifrons, Bathyclarias worthingtoni, Bathygobius casamancus, Bathygobius fuscus, Bathygobius petrophilus, Bathygobius samberanoensis, Bathygobius soporator, Bedotia albomarginata, Bedotia alveyi, Bedotia geayi, Bedotia leucopteron, Bedotia longianalis, Bedotia madagascariensis, Bedotia marojejy, Bedotia masoala, Bedotia tricolor, Belonoglanis brieni, Belonoglanis tenuis, Belonophago hutsebouti, Belonophago tinanti, Benitochromis batesii, Benitochromis conjunctus, Benitochromis finleyi, Benitochromis nigrodorsalis, Benitochromis riomuniensis, Benitochromis ufermanni, Benthochromis melanoides, Benthochromis tricoti, Boleophthalmus boddarti, Bostrychus africanus, Boulengerochromis microlepis, Boulengeromyrus knoepffleri, Brachyalestes bimaculatus, Brachyalestes carolinae, Brachyalestes comptus, Brachyalestes fwaensis, Brachyalestes imberi, Brycinus imberi, Brachyalestes jacksonii, Brachyalestes kingsleyae, Brachyalestes nurse, Brachypetersius altus, Brachypetersius cadwaladeri, Brachypetersius gabonensis, Brachypetersius huloti, Brachypetersius pseudonummifer, Brevimyrus niger, Brienomyrus brachyistius)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((10.0615 -3.4463,10.1382 -3.5292,10.1382 2.0599,9.2753 2.0599,9.2723 2.0399,8.8555 1.2955,8.8103 -0.1351,8.354 -0.2687,8.2157 -0.7924,8.7426 -1.8029,8.6574 -2.0749,8.8035 -2.4281,9.149 -2.574,10.0615 -3.4463))"
 ]
}

 The dataset includes 38 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006062-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.