cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/qrcjq-2hg86
title: V. cholerae RT4236 (stationary)

description: Classical strain with ctxA deletion.Cell harbors pMT5 plasmid (inducible toxT).
description: <strong>Tilt Series Date:</strong> 2015-05-11</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, 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> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> SIRT</p>
<strong>Collaborators and Roles:</strong> Strain from Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Overnight cultures of Vibrio cholerae O395 NI pMT5 grown in LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 finder.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-18/3dimage_73304/</p>20150511_AK07_10018_SIRT_2K.rec,  Reconstruction (Pixel Size 0.0 nm), 5.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150511_AK07_10018.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/ycw2015-05-11-18/rawdata/20150511_AK07_10018.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.hd4v6r
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex depressa transsilvanica"
 ]
}

 The dataset includes 89 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002725-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/zda1w-fra19
title: Coxiella_ Verocells_28dpi

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Coxiella cells purified from infected Vero cells.
description: <strong>Tilt Series Date:</strong> 2017-10-19</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </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> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal and Mohammed Kaplan using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Refer to Heinzen lab.</p>
<strong>Sample Preparation:</strong> Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-19-69/rawdata/</p>Cb_vero_20171019b0066.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Cb_vero_20171019b0066_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/e07sf-qgb32
title: Coxiella_ Verocells_28dpi

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Coxiella cells purified from infected Vero cells.
description: <strong>Tilt Series Date:</strong> 2017-10-19</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </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> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal and Mohammed Kaplan using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Refer to Heinzen lab.</p>
<strong>Sample Preparation:</strong> Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-19-87/rawdata/</p>Cb_vero_20171019b0084.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Cb_vero_20171019b0084_part61_1.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/a00n3-6az30
title: Coxiella_ Verocells_28dpi

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Coxiella cells purified from infected Vero cells.
description: <strong>Tilt Series Date:</strong> 2017-09-25</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </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> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Refer to Heinzen lab.</p>
<strong>Sample Preparation:</strong> Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.T</p>
  dga2017-09-25-14_slicer18922.jpg: multilayered structure beneath the inner membrane
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-09-25-14/rawdata/</p>Cb_vero_201709250014.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Cb_vero_201709250014.rec,  Reconstruction (Pixel Size 1.56 nm), 889.0 MB  
        
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DOI: 10.22002/wve50-2c553
title: Thermococcus koakarensis

description: Imaging Thermococcus koakarensis flagella
description: <strong>Tilt Series Date:</strong> 2016-09-20</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Thermococcus kodakarensis</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: 140.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </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> Strain sent to us by Robert Gunsalus, UCLA. Data collected and processed by Kiwoo and Debnath Ghosal</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Standard Tk medium with starch and sulfur</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the this strain. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3.5 sec. Wait time 8 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-09-20-5/3dimage_79333/</p>atlas10004_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/dga2016-09-20-5/3dimage_79333/atlas10004_full.rec"
        > <i class="download icon"></i> Download </a></p>

        atlas10004.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/dga2016-09-20-5/rawdata/atlas10004.mrc"
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DOI: 10.15468/dl.cnk4vn
title: Occurrence Download

description: A dataset containing 945 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea vanhouttei",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 945 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002730-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6bw4q8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea vanhouttei",
 "Country is Slovakia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002728-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/gk66y-4ph04
title: Coxiella_ Verocells_28dpi

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Coxiella cells purified from infected Vero cells.
description: <strong>Tilt Series Date:</strong> 2017-09-25</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </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> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Refer to Heinzen lab.</p>
<strong>Sample Preparation:</strong> Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.T</p>
  dga2017-09-25-84_slicer19022.jpg: multilayer structure beneath the inner membrane
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-09-25-84/rawdata/</p>Cb_vero_201709250084.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Cb_vero_201709250084_part61_4.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/kvg3c-6vf80
title: perfusiondcrp_fixd_good track

description: MOh and Sahand
description: <strong>Tilt Series Date:</strong> 2015-08-24</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</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: -8.0 μm,  magnification: 27500x. </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> The sample was grown in perfusion chamber and fixed for 30 minutes with 4% formaldehyde. Then washed 3 times in distilled water for 1 minute each. The sample was blotted in a manual plunger with 1.5ul gold beads.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lm is taken before and after fixing. In the LM after fixing the nanowires were shrunk. Although the cells looked good with formaldehyde we had lost long nanowires. 2 squares were imaged with correlation anyway.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-08-24-16/rawdata/</p>perfusiondcrp_sq130008.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        perfusiondcrp_sq130008_part121_25.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.gegm75
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea vanhouttei",
 "Country is Poland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 92 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002727-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ycmyv-k1v11
title: M. xanthus knockout minor pilins

description: Grid box YWC130Strain SA6815
description: <strong>Tilt Series Date:</strong> 2015-04-26</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</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: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </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> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 2 days in 220 rpm shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 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/ycw2015-04-26-43/rawdata/</p>20150426_YWC130_10049.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150426_YWC130_10049_part121_2.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/m3tke-beg88
title: V. cholerae JAS290 delta-tcpS

description: Classical strain with ctxA deletionStrain name JAS290 (tcpS gene knockout)Cell harbors pMT5 plasmid (inducible toxT)
description: <strong>Tilt Series Date:</strong> 2016-08-07</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </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> Strain from Gabriela Kovacikova</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O/N cultures of Vibrio cholerae O395 N1 pMT5 grown in LB, 1 mM IPTG and 100 ug/mL ampicillin.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3.5µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 3 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/ycw2016-08-07-14/rawdata/</p>20160807_YWC217_10014.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        20160807_YWC217_10014_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/2f24k-88c67
title: V. cholerae JAS286 delta-tcpD

description: Classical strain with ctxA deletionStrain name JAS286 (tcpD gene knonkout)Cell harbors pMT5 plasmid (inducible toxT)
description: <strong>Tilt Series Date:</strong> 2016-08-05</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </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> Strain from Gabriela Kovacikova</p>
<strong>Purification / Growth Conditions / Treatment:</strong> O/N cultures of Vibrio cholerae O395 N1 pMT5 grown in LB, 1 mM IPTG and 100 ug/mL ampicillin.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3.5µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 3 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/ycw2016-08-05-29/rawdata/</p>20160805_YWC215_10029.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        20160805_YWC215_10029_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>