cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.49jkqu
title: Occurrence Download

description: A dataset containing 2205 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tapirella bairdii (Gill, 1865)"
 ]
}

 The dataset includes 2205 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030950-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9p5rf
title: Occurrence Download

description: A dataset containing 31691 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trapa natans L."
 ]
}

 The dataset includes 31691 records from 537 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030704-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xd7pe2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Magallana gigas",
 "Country is Tonga",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033016-250811113504898/datasets/export for details.
DOI: 10.22002/w8xtt-s1m44
title: Xanthomonas (-B7) vs Caulobacter

description: Xanthomonas ΔVirB7 Vs Caulobacter competition
description: <strong>Tilt Series Date:</strong> 2017-03-16</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: (-54.0°, 54.0°), 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 (-VirB7) 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= 9 sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-16-9/rawdata/</p>DeltaVirB7_Cc_20170316a0013.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-16-9/rawdata/DeltaVirB7_Cc_20170316a0013.mrc"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316a0013_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-16-9/3dimage_109156/DeltaVirB7_Cc_20170316a0013_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316a0013.ali,  392.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-16-9/file_25893/DeltaVirB7_Cc_20170316a0013.ali"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316a0013.tlt,  440.0 B  
        
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        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316a0013_fid.tlt,  440.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/fwq4f-aq495
title: Xanthomonas (-B7) vs Caulobacter

description: Xanthomonas ΔVirB7 Vs Caulobacter competition
description: <strong>Tilt Series Date:</strong> 2017-03-17</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: 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 (-VirB7) 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= 9 sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-17-1/rawdata/</p>DeltaVirB7_Cc_20170316na0001.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-17-1/rawdata/DeltaVirB7_Cc_20170316na0001.mrc"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316na0001_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316na0001.ali,  299.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-17-1/file_25899/DeltaVirB7_Cc_20170316na0001.ali"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316na0001.tlt,  336.0 B  
        
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        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316na0001_fid.tlt,  336.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/btp4h-89779
title: H. Neapolitanus Carboxysomes

description: Carboxysomes purified from H. Neapolitanus, WT, high resolution
description: <strong>Tilt Series Date:</strong> 2019-08-21</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Halothiobacillus neapolitanus</p>
<strong>Strain:</strong> c2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: 0.0 μm,  magnification: 81000x. </p>
<strong>Microscope:</strong> None</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD, ctffind4, novaCTF, custom bash and Matlab scripts</p>
<strong>Collaborators and Roles:</strong> purified by Tom Laughlin in the Savage lab at Berkeley; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified by the Savage lab</p>
<strong>Sample Preparation:</strong> protochip C-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity, defocus varying -1 to -5.5 microns</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-48/rawdata/</p>48_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 4.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-48/rawdata/48_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        48_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 344.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-48/3dimage_113107/48_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_48.mrc.mdoc,  30.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-48/rawdata/TS_48.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-48/file_26701/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 13.5 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-48/file_26702/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/70cdh-sxc35
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: (-52.0°, 52.0°), 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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-7/rawdata/</p>Xac_Cc_20170309_tgt00010001.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-7/rawdata/Xac_Cc_20170309_tgt00010001.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309_tgt00010001_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_20170309_tgt00010001.ali,  377.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309_tgt00010001.tlt,  424.0 B  
        
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        Xac_Cc_20170309_tgt00010001_fid.tlt,  424.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/eh376-hxy61
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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-12/rawdata/</p>Xac_Cc_20170309a0011.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/dga2017-03-09-12/rawdata/Xac_Cc_20170309a0011.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0011_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-12/3dimage_109106/Xac_Cc_20170309a0011_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0011.ali,  434.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-12/file_25743/Xac_Cc_20170309a0011.ali"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0011.tlt,  488.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-12/file_25746/Xac_Cc_20170309a0011.tlt"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0011_fid.tlt,  488.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-12/file_25748/Xac_Cc_20170309a0011_fid.tlt"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.8vh9rw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Magallana gigas",
 "Country is Tunisia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033019-250811113504898/datasets/export for details.
DOI: 10.22002/x929s-ajt72
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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-49/rawdata/</p>Xac_Cc_20170309a0047.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/dga2017-03-09-49/rawdata/Xac_Cc_20170309a0047.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0047_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_20170309a0047.ali,  434.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-49/file_25821/Xac_Cc_20170309a0047.ali"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0047.tlt,  488.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-49/file_25824/Xac_Cc_20170309a0047.tlt"
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        Xac_Cc_20170309a0047_fid.tlt,  488.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-49/file_25826/Xac_Cc_20170309a0047_fid.tlt"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/sf818-kcw48
title: Xanthomonas vs E.coli (Br)

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs E.coli (Br)These are correlated tomograms.
description: <strong>Tilt Series Date:</strong> 2017-03-08</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: (-52.0°, 52.0°), 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 E.coli (Br) 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 15 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot time= 6 sec</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-08-8/rawdata/</p>Xac_wt_20170308_V4_tgt00010005.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/dga2017-03-08-8/rawdata/Xac_wt_20170308_V4_tgt00010005.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_wt_20170308_V4_tgt00010005_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-08-8/3dimage_109100/Xac_wt_20170308_V4_tgt00010005_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xac_wt_20170308_V4_tgt00010005.ali,  292.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xac_wt_20170308_V4_tgt00010005.tlt,  328.0 B  
        
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        Xac_wt_20170308_V4_tgt00010005_fid.tlt,  328.0 B  
        
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