cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/zn6t5-1yj52
title: Xanthomonas WT

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9)
description: <strong>Tilt Series Date:</strong> 2017-03-03</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 200.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the strain, data collected by Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in 2xTY with apt antibiotics, freeze cells next day after about 14 hour when they are in stationary phase.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot time= 5 sec. ** Use 7 sec for next sessions.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-03-12/rawdata/</p>Xac_wt_20170303b10016.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-03-12/rawdata/Xac_wt_20170303b10016.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_wt_20170303b10016_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xac_wt_20170303b10016.ali,  577.3 MB  
        
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        Xac_wt_20170303b10016.tlt,  648.0 B  
        
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        Xac_wt_20170303b10016_fid.tlt,  648.0 B  
        
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DOI: 10.22002/kq6n4-bs833
title: Xanthomonas vs Caulobacter

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter competition
description: <strong>Tilt Series Date:</strong> 2017-03-30</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1.5°, constant angular increment, dosage: 160.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the strains, data collected by Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot time= 10 sec</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-30-27/rawdata/</p>Xac_Cc_2017032910tha0019.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.0 GB  
        
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        Xac_Cc_2017032910tha0019_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xac_Cc_2017032910tha0019.ali,  384.9 MB  
        
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        Xac_Cc_2017032910tha0019.tlt,  432.0 B  
        
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        Xac_Cc_2017032910tha0019_fid.tlt,  432.0 B  
        
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DOI: 10.22002/dc723-zsp70
title: Xanthomonas vs Caulobac (-T1SS)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter (delta-cdzAB) competition. Caulobacter strain is a T1SS deletion strain.
description: <strong>Tilt Series Date:</strong> 2017-10-27</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the Xac strain, Caulobacter strain is from Laub lab. Data collected and processed by Mohammed Kaplan and Debnath Ghosal</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Manual blotting, humidity 100%</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-27-25/rawdata/</p>Xan_CaulDelT1_20172710h0001.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        Xan_CaulDelT1_20172710h0001_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xan_CaulDelT1_20172710h0001.ali,  399.1 MB  
        
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        Xan_CaulDelT1_20172710h0001.tlt,  448.0 B  
        
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        Xan_CaulDelT1_20172710h0001_fid.tlt,  448.0 B  
        
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DOI: 10.15468/dl.cpfc35
title: Occurrence Download

description: A dataset containing 14300 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is California",
 "TaxonKey is Vanessa cardui",
 "Year 2005-2025"
 ]
}

 The dataset includes 14300 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033017-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/z03fg-2ms93
title: Xanthomonas vs Caulobac (-T1SS)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter (delta-cdzAB) competition. Caulobacter strain is a T1SS deletion strain.
description: <strong>Tilt Series Date:</strong> 2017-10-27</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the Xac strain, Caulobacter strain is from Laub lab. Data collected and processed by Mohammed Kaplan and Debnath Ghosal</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Manual blotting, humidity 100%</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-27-15/rawdata/</p>Xan_CaulDelT1_20172710g0003.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        Xan_CaulDelT1_20172710g0003_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xan_CaulDelT1_20172710g0003.ali,  370.6 MB  
        
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        Xan_CaulDelT1_20172710g0003.tlt,  416.0 B  
        
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        Xan_CaulDelT1_20172710g0003_fid.tlt,  416.0 B  
        
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DOI: 10.22002/evsvc-95g93
title: Xanthomonas vs Caulobac (-T1SS)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter (delta-cdzAB) competition. Caulobacter strain is a T1SS deletion strain.
description: <strong>Tilt Series Date:</strong> 2017-10-27</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the Xac strain, Caulobacter strain is from Laub lab. Data collected and processed by Mohammed Kaplan and Debnath Ghosal</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Manual blotting, humidity 100%</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-27-22/rawdata/</p>Xan_CaulDelT1_20172710g0010.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        Xan_CaulDelT1_20172710g0010_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xan_CaulDelT1_20172710g0010.ali,  370.6 MB  
        
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        Xan_CaulDelT1_20172710g0010.tlt,  416.0 B  
        
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        Xan_CaulDelT1_20172710g0010_fid.tlt,  416.0 B  
        
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DOI: 10.22002/gw0x7-fae98
title: Coxiella burnetii_wt_D15

description: Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-15  culture.
description: <strong>Tilt Series Date:</strong> 2016-11-04</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: 1.5°, constant angular increment, dosage: 130.0 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> TOMO3D</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> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab</p>
  dga2016-11-04-31_slicer17274.jpg: storage granule dga2016-11-04-31_slicer17704.jpg: A bacteria-like structure in Coxiella burnetii .  Intrabacterial bacterium .  Endosymbiont
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-31/rawdata/</p>15D_Pos4_atlas20002.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
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        15D_Pos4_atlas20002_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        15D_Pos4_atlas20002.ali,  570.2 MB  
        
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        15D_Pos4_atlas20002.tlt,  640.0 B  
        
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        15D_Pos4_atlas20002_fid.tlt,  640.0 B  
        
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DOI: 10.22002/5msq6-3ga74
title: Xanthomonas vs Caulobac (-T1SS)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter (delta-cdzAB) competition. Caulobacter strain is a T1SS deletion strain.
description: <strong>Tilt Series Date:</strong> 2017-10-31</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Chuck Farah lab made the Xac strain, Caulobacter strain is from Laub lab. Data collected and processed by Mohammed Kaplan and Debnath Ghosal</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Manual blotting, humidity 100%. 10 nm gold in 5% BSA. 4 ul Gold was applied onto the grid and blotted manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-31-89/rawdata/</p>Xan_CaulDelT1_20172710m0003.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        Xan_CaulDelT1_20172710m0003_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xan_CaulDelT1_20172710m0003.ali,  335.0 MB  
        
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        Xan_CaulDelT1_20172710m0003.tlt,  376.0 B  
        
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        Xan_CaulDelT1_20172710m0003_fid.tlt,  376.0 B  
        
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