cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/zx0kj-r9k85
title: Caulobacter crescentus

description: Raw data files of Caulobacter crescentus
description: <strong>Tilt Series Date:</strong> 2018-07-10</p>
<strong>Data Taken By:</strong> Lujia Zhang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</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> For the research of pilus, over-express, from Partick, 4331</p>
<strong>Purification / Growth Conditions / Treatment:</strong> swarmer cell, PVP</p>
<strong>Sample Preparation:</strong> force 4, time 6, humidity 100%, temp. 22</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-07-10-19/rawdata/</p>targ13.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-07-10-19/rawdata/targ13.mrc"
        > <i class="download icon"></i> Download </a></p>

        targ13_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-07-10-19/3dimage_100094/targ13_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/wwx73-tcd41
title: C. crescentus NA1000 Tad pilus

description: C. crescentus NA1000 Tad pilus project. The goad is to get an STA of the Tad pilus secretion system.
description: <strong>Tilt Series Date:</strong> 2019-08-17</p>
<strong>Data Taken By:</strong> Steven Wang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 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> None</p>
<strong>Collaborators and Roles:</strong> Patrick Viollier and Lujia Zhang</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Swarmer cells purified using Percoll (colloidal silica). Cultured using M2G media.</p>
<strong>Sample Preparation:</strong> 10 nm gold beads. Blotting force 4, blotting time 4, draining time 1. Quantifoil copper grids.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-08-17-34/rawdata/</p>caulobacter_na1000_wt_035_af.mrc,  Tilt Series (Pixel Size 0.336 nm), 3.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        caulobacter_na1000_wt_035_af.mrc.mdoc,  815.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.18739/a2nk36715
title: Collected data for Shin et al. (2025): Nutrient limitation induces a productivity decline from light-controlled maximum in Greenland streams (2022-2023)

description: This resource contains chlorophyll-a measurement from nutrient diffusion substrate experiments conducted in Greenland streams in 2022-23. In 2022, Nutrient diffusion substrate was deployed in five streams twice (early and late summer). In 2023, we conducted continuous dosing experiments in one of the five streams, where the dosing separated the reach into three segments (control, nitrogen (+N), nitrogen and phosphorous (+NP)). The nutrient diffusion substrate was deployed in these three segments. Along with nutrient diffusion substrate results, abiotic factors (light, water temperature, and discharge) were also continuously monitored during deployments. These data were used to develop an evaluation tool (described in Shin et al., 2025) for nutrient limitations that are based on declines away from a maximum productivity caused by the lack of nutrient amendments to nutrient diffusion substrate experiments.
DOI: 10.22002/v1jky-85403
title: Caulobacter crescentus

description: Raw data files of Caulobacter crescentus
description: <strong>Tilt Series Date:</strong> 2018-10-08</p>
<strong>Data Taken By:</strong> Lujia Zhang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 252.8 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</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> For the research of pilus, Del E from Partick</p>
<strong>Purification / Growth Conditions / Treatment:</strong> swarmer cell, PVP</p>
<strong>Sample Preparation:</strong> force 4, time 6, humidity 100%, temp. 22</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-08-3/rawdata/</p>targ03.mrc,  Tilt Series (Pixel Size 0.3712 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        targ03_full.rec,  Reconstruction (Pixel Size 1.4848 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-08-3/3dimage_99491/targ03_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/zrf4x-xm792
title: P. gingivalis PorV mutant

description: Raw data files of P. gingivalis PorV mutant
description: <strong>Tilt Series Date:</strong> 2019-01-23</p>
<strong>Data Taken By:</strong> Georges Chreifi</p>
<strong>Species / Specimen:</strong> Porphyromonas gingivalis</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</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> Eric Reynolds</p>
<strong>Sample Preparation:</strong> Liquid culture. Harvested and plunge-frozen in late phase.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2019-01-23-9/rawdata/</p>2-PorV-17.mrc,  Tilt Series (Pixel Size 0.3519 nm), 1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2019-01-23-9/rawdata/2-PorV-17.mrc"
        > <i class="download icon"></i> Download </a></p>

        2-PorV-17_full.rec,  Reconstruction (Pixel Size 1.4076 nm), 267.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2019-01-23-9/3dimage_100513/2-PorV-17_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7fp7a-15m46
title: ec4-2

description: EC4-2, sq1, IT 1.5s
description: <strong>Tilt Series Date:</strong> 2018-07-12</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 1094</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> E.Coli 1094 was grown at approx OD 0.8 before freezing</p>
<strong>Sample Preparation:</strong> Both sides autoblotting - BT 4s - BF 0 - 22deg - 100% hum</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2018-07-12-10/rawdata/</p>sq1_cell4.mrc,  Tilt Series (Pixel Size 0.54 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2018-07-12-10/rawdata/sq1_cell4.mrc"
        > <i class="download icon"></i> Download </a></p>

        sq1_cell4_part61_7.rec,  Reconstruction (Pixel Size 1.08 nm), 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2018-07-12-10/3dimage_93196/sq1_cell4_part61_7.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/30cb7-has55
title: Caulobacter delta-CpaF

description: Tad pilus system
description: <strong>Tilt Series Date:</strong> 2019-02-15</p>
<strong>Data Taken By:</strong> Steven Wang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> AM369, ΔldpF</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 193.8 eV/Å²,  defocus: -6.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> iMOD</p>
<strong>Collaborators and Roles:</strong> Patrick Viollier who provided WT and mutants</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 28 degrees Celsius</p>
<strong>Sample Preparation:</strong> plunge-freezing</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-02-15-14/rawdata/</p>stalk_4.mrc,  Tilt Series (Pixel Size 0.351 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-02-15-14/rawdata/stalk_4.mrc"
        > <i class="download icon"></i> Download </a></p>

        stalk_4_full.rec,  Reconstruction (Pixel Size 1.404 nm), 356.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-02-15-14/3dimage_101594/stalk_4_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/s4e2d-r5013
title: Caulobacter delta-CpaF

description: Raw data files of Caulobacter delta-CpaF
description: <strong>Tilt Series Date:</strong> 2019-01-08</p>
<strong>Data Taken By:</strong> Steven Wang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 183.0 eV/Å²,  defocus: -9.0 μm,  magnification: 42000x. </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> iMOD</p>
<strong>Collaborators and Roles:</strong> Patrick Viollier</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 28 degrees celsius</p>
<strong>Sample Preparation:</strong> plunge-freezing</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-01-08-39/rawdata/</p>targ67.mrc,  Tilt Series (Pixel Size 0.351 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-01-08-39/rawdata/targ67.mrc"
        > <i class="download icon"></i> Download </a></p>

        targ67_full.rec,  Reconstruction (Pixel Size 1.404 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-01-08-39/3dimage_100861/targ67_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/e7vh2-hbz02
title: C. crescentus NA1000 Tad pilus

description: C. crescentus NA1000 Tad pilus project. The goad is to get an STA of the Tad pilus secretion system.
description: <strong>Tilt Series Date:</strong> 2019-08-17</p>
<strong>Data Taken By:</strong> Steven Wang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 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> None</p>
<strong>Collaborators and Roles:</strong> Patrick Viollier and Lujia Zhang</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Swarmer cells purified using Percoll (colloidal silica). Cultured using M2G media.</p>
<strong>Sample Preparation:</strong> 10 nm gold beads. Blotting force 4, blotting time 4, draining time 1. Quantifoil copper grids.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-08-17-80/rawdata/</p>caulobacter_na1000_wt_081_af.mrc,  Tilt Series (Pixel Size 0.336 nm), 3.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        caulobacter_na1000_wt_081_af.mrc.mdoc,  813.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/srv9n-8nd16
title: P. gingivalis wild type

description: Raw data files of P. gingivalis wild type
description: <strong>Tilt Series Date:</strong> 2020-11-06</p>
<strong>Data Taken By:</strong> Georges Chreifi</p>
<strong>Species / Specimen:</strong> Porphyromonas gingivalis</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 170.0 eV/Å²,  defocus: -6.0 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> Eric Reynolds</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown and harvested from plates</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2020-11-06-242/rawdata/</p>PginWT9_241.mrc,  Tilt Series (Pixel Size 0.333 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2020-11-06-242/rawdata/PginWT9_241.mrc"
        > <i class="download icon"></i> Download </a></p>

        PginWT9_241_part41_6.rec,  Reconstruction (Pixel Size 1.332 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/93aex-keq85
title: C. crescentus NA1000 Tad pilus

description: C. crescentus NA1000 Tad pilus project. The goad is to get an STA of the Tad pilus secretion system.
description: <strong>Tilt Series Date:</strong> 2019-08-17</p>
<strong>Data Taken By:</strong> Steven Wang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 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> None</p>
<strong>Collaborators and Roles:</strong> Patrick Viollier and Lujia Zhang</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Swarmer cells purified using Percoll (colloidal silica). Cultured using M2G media.</p>
<strong>Sample Preparation:</strong> 10 nm gold beads. Blotting force 4, blotting time 4, draining time 1. Quantifoil copper grids.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-08-17-107/rawdata/</p>caulobacter_na1000_wt_108_af.mrc,  Tilt Series (Pixel Size 0.336 nm), 3.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        caulobacter_na1000_wt_108_af.mrc.mdoc,  812.0 B  
        
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DOI: 10.15468/dl.mwwdfm
title: Occurrence Download

description: A dataset containing 54121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phalaris canariensis villosula, Phalaris canariensis vivipara, Phalaris canariensis debilis, Phalaris canariensis nigra, Phalaris canariensis subcylindrica, Phalaris canariensis tenuis, Phalaris canariensis villosula, Phalaris ovata, Phleum alpinum, Phleum alpinum alpinum, Phleum alpinum bracteolatum, Phleum alpinum subcapitatum, Phleum alpinum alpinum, Phleum alpinum ambiguum, Phleum alpinum americanum, Phleum alpinum bracteolatum, Phleum alpinum commutatum, Phleum alpinum commutatum, Phleum alpinum commutatum, Phleum alpinum commutatum, Phleum alpinum parviceps, Phleum alpinum rhaeticum, Phleum alpinum scribnerianum, Phleum alpinum subcapitatum, Phleum alpinum tenue, Phleum alpinum alpinum, Phleum alpinum ambiguum, Phleum alpinum americanum, Phleum alpinum commutatum, Phleum alpinum commutatum, Phleum alpinum commutatum, Phleum alpinum commutatum, Phleum alpinum foliosum, Phleum alpinum nigricans, Phleum alpinum parviceps, Phleum alpinum scribnerianum, Phleum alpinum scribnerianum, Phleum alpinum subcapitatum, Phleum alpinum tenue, Phleum arcticum, Phleum arcticum, Phleum capitatum, Phleum commutatum, Phleum commutatum americanum, Phleum commutatum americanum, Phleum commutatum commutatum, Phleum geniculatum, Phleum gerardii, Phleum haenkeanum, Phleum mouterdei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Continent is Europe",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 54121 records from 270 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047379-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rb99s3
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-20.07518 45.16371,14.07518 45.16371,14.07518 58.83629,-20.07518 58.83629,-20.07518 45.16371))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Neuropteridae"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047423-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/m4vs9-8rt83
title: Caulobacter crescentus

description: Raw data files of Caulobacter crescentus
description: <strong>Tilt Series Date:</strong> 2018-10-17</p>
<strong>Data Taken By:</strong> Lujia Zhang</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 252.8 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</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> For the research of pilus, Del E from Partick</p>
<strong>Purification / Growth Conditions / Treatment:</strong> swarmer cell, PVP</p>
<strong>Sample Preparation:</strong> force 4, time 6, humidity 100%, temp. 22</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-17-52/rawdata/</p>targ50.mrc,  Tilt Series (Pixel Size 0.3712 nm), 3.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-17-52/rawdata/targ50.mrc"
        > <i class="download icon"></i> Download </a></p>

        targ50_full.rec,  Reconstruction (Pixel Size 1.4848 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lza2018-10-17-52/3dimage_99634/targ50_full.rec"
        > <i class="download icon"></i> Download </a></p>