cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.y39a2r
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neslia paniculata",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 47 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040720-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16938155
title: Supplementary Materials for "Increasing Residence Time in Random Packed Beds of Spheres with a Helical Flow Deflector"
DOI: 10.5281/zenodo.16938156
title: Supplementary Materials for "Increasing Residence Time in Random Packed Beds of Spheres with a Helical Flow Deflector"
DOI: 10.15468/dl.wnaxju
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhinella roqueana"
 ]
}

 The dataset includes 157 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040722-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w77vng
title: Occurrence Download

description: A dataset containing 540 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-88.92769 21.38755,-88.89413 21.39311,-88.89413 21.39327,-88.89287 21.39345,-88.8926 21.39365,-88.89186 21.39391,-88.89164 21.39402,-88.89135 21.39407,-88.89043 21.39416,-88.88898 21.39437,-88.88649 21.39459,-88.88555 21.39487,-88.88506 21.39525,-88.88499 21.39548,-88.8843 21.39567,-88.88327 21.39572,-88.8823 21.39579,-88.88125 21.39569,-88.88038 21.39573,-88.88023 21.39579,-88.88006 21.39696,-88.87972 21.39783,-88.87967 21.39621,-88.87885 21.39592,-88.87809 21.39584,-88.87699 21.39575,-88.87642 21.39567,-88.87597 21.39587,-88.87582 21.3956,-88.87532 21.3962,-88.87357 21.39615,-88.87064 21.39587,-88.86878 21.39666,-88.85937 21.39582,-88.85494 21.39651,-88.85402 21.39693,-88.85307 21.39727,-88.85137 21.39757,-88.84889 21.3985,-88.84232 21.3987,-88.84175 21.39861,-88.84085 21.39899,-88.84059 21.39866,-88.83938 21.39977,-88.83864 21.40038,-88.8376 21.40068,-88.83098 21.40194,-88.82509 21.40451,-88.82477 21.40558,-88.82351 21.40621,-88.82194 21.40728,-88.81891 21.40796,-88.81715 21.40905,-88.81421 21.41048,-88.81099 21.4106,-88.80317 21.41251,-88.79889 21.41262,-88.79879 21.41404,-88.79716 21.41654,-88.79714 21.41688,-88.80047 21.4135,-88.80091 21.4163,-88.79929 21.41853,-88.80134 21.4199,-88.7873 21.42323,-88.73931 21.43227,-88.69786 21.45295,-88.67956 21.46889,-88.6551 21.48574,-88.63906 21.50086,-88.63074 21.51068,-88.63113 21.51136,-88.63134 21.51289,-88.63113 21.51346,-88.61641 21.52303,-88.59659 21.52651,-88.55972 21.53268,-88.554 21.53383,-88.54803 21.53452,-88.54709 21.53558,-88.54315 21.53569,-88.5243 21.53563,-88.50906 21.5394,-88.49022 21.54815,-88.39519 21.56767,-88.35202 21.72944,-88.89965 21.70301,-88.91388 21.44451,-88.92769 21.38755))",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Annelida, Platyhelminthes, Crustacea, Mollusca, Echinodermata)"
 ]
}

 The dataset includes 540 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040723-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/m1169-hnm93
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> 2017-10-21</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: 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> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-31/rawdata/</p>Xan_CaulDelT1_20172110b0006.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-31/rawdata/Xan_CaulDelT1_20172110b0006.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110b0006_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110b0006.ali,  292.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-31/file_25660/Xan_CaulDelT1_20172110b0006.ali"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110b0006.tlt,  328.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-31/file_25661/Xan_CaulDelT1_20172110b0006.tlt"
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        Xan_CaulDelT1_20172110b0006_fid.tlt,  328.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/0paa1-kee83
title: Xanthomonas vs minicells

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Ec-mini cells
description: <strong>Tilt Series Date:</strong> 2017-04-27</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: (-53.0°, 53.0°), step: 1.5°, constant angular increment, dosage: 120.0 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 Ec-mini 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 https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-55/rawdata/</p>Xac-mini-20170427x30008.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-55/rawdata/Xac-mini-20170427x30008.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427x30008_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-mini-20170427x30008.ali,  506.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-55/file_26271/Xac-mini-20170427x30008.ali"
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        Xac-mini-20170427x30008.tlt,  568.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-55/file_26272/Xac-mini-20170427x30008.tlt"
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        Xac-mini-20170427x30008_fid.tlt,  568.0 B  
        
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DOI: 10.22002/cckma-y1f31
title: Xanthomonas vs Caulobacter

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter competition
description: <strong>Tilt Series Date:</strong> 2017-03-09</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: 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>
  dga2017-03-09-24_slicer17987.jpg: t4ss?
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-24/rawdata/</p>Xac_Cc_20170309a0028.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-24/rawdata/Xac_Cc_20170309a0028.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0028_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_Cc_20170309a0028.ali,  413.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-24/file_25791/Xac_Cc_20170309a0028.ali"
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        Xac_Cc_20170309a0028.tlt,  464.0 B  
        
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        Xac_Cc_20170309a0028_fid.tlt,  464.0 B  
        
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DOI: 10.22002/tbaws-pkw54
title: Xanthomonas vs minicells

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Ec-mini cells
description: <strong>Tilt Series Date:</strong> 2017-04-27</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: (-53.0°, 53.0°), step: 1.5°, constant angular increment, dosage: 120.0 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 Ec-mini 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 https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-38/rawdata/</p>Xac-mini-20170427w10002.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-38/rawdata/Xac-mini-20170427w10002.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427w10002_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-mini-20170427w10002.ali,  506.0 MB  
        
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        Xac-mini-20170427w10002.tlt,  568.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-38/file_26242/Xac-mini-20170427w10002.tlt"
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        Xac-mini-20170427w10002_fid.tlt,  568.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xy0za-qrb55
title: Staphylococcus aureus_WT

description: T7SS
description: <strong>Tilt Series Date:</strong> 2017-06-29</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: (-50.0°, 50.0°), step: 1.5°, constant angular increment, dosage: 280.0 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 Tracy Palmer, University of Dundee. Data collected and processed by Ki Woo and Debnath Ghosal.</p>
<strong>Sample Preparation:</strong> Media: TSA 500g (Oxoid TSA and TSB from Thermo Fisher. 10525943), TBS 500g (10137562)Dilute an overnight culture 1/100Incubate it for 4 hr (--> OD 2)Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-06-29-39/rawdata/</p>Saureus_WT_06290028.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-06-29-39/rawdata/Saureus_WT_06290028.mrc"
        > <i class="download icon"></i> Download </a></p>

        Saureus_WT_06290028_part67_15.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        dga2017-06-29-39_slicer18621.png, , 684.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/dga2017-06-29-39_slicer18621.png"
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        dga2017-06-29-39_slicer18622.png, , 711.4 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/dga2017-06-29-39_slicer18622.png"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/93jam-xgr38
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> 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> 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>
  dga2016-11-04-94_slicer17266.jpg: lamellation
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-94/3dimage_79707/</p>15D_Pos4_atlas20065_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/dga2016-11-04-94/3dimage_79707/15D_Pos4_atlas20065_full.rec"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20065.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/dga2016-11-04-94/rawdata/15D_Pos4_atlas20065.mrc"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20065.tlt,  648.0 B  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20065_fid.tlt,  648.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3s76w-7cn20
title: U2OS-Tubulin Tracker Green

description: U2OS cells stained with tubulin tracker to locate midbodies. Cryo-FIB milling is used to make the sample thinner.
description: <strong>Tilt Series Date:</strong> 2017-06-13</p>
<strong>Data Taken By:</strong> Wei Zhao</p>
<strong>Species / Specimen:</strong> U2OS</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, 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> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD-patch tracking</p>
<strong>Purification / Growth Conditions / Treatment:</strong> U2OS cells grown on Au finder grids for 28-48 hours.Grids coated with PL.</p>
<strong>Sample Preparation:</strong> Cells were stained with tubulin tracker and Hoechst before freezing. Plunge frozen using the vitrobot III blotted manually from back(drain time 1s).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wza2017-06-13-3/rawdata/</p>TS2.mrc,  Tilt Series (Pixel Size 0.371 nm), 1.7 GB  
        
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        TS2_bin2.rec,  Reconstruction (Pixel Size 0.0 nm), 215.6 MB  
        
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        wza2017-06-13-3_slicer18432.png,  Mitochondron, 1.2 MB  
        
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        wza2017-06-13-3_slicer18433.png,  Interface between autophagosome and ER, 913.7 kB  
        
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