cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/011m8-b8q77
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/dga2017-10-27-9/rawdata/</p>Xan_CaulDelT1_20172710c0007.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/dga2017-10-27-9/rawdata/Xan_CaulDelT1_20172710c0007.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172710c0007_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_20172710c0007.ali,  356.4 MB  
        
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        Xan_CaulDelT1_20172710c0007.tlt,  400.0 B  
        
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        Xan_CaulDelT1_20172710c0007_fid.tlt,  400.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/d8rgg-pkj57
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>
  dga2016-11-04-43_slicer17254.jpg: feeding tube between a mother cell and a mebrane vesicle? dga2016-11-04-43_slicer17255.jpg: T4SS at the cell pole
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-43/rawdata/</p>15D_Pos4_atlas20014.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/dga2016-11-04-43/rawdata/15D_Pos4_atlas20014.mrc"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20014_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20014.ali,  577.3 MB  
        
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        15D_Pos4_atlas20014.tlt,  648.0 B  
        
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        15D_Pos4_atlas20014_fid.tlt,  648.0 B  
        
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DOI: 10.15468/dl.t9x582
title: Occurrence Download

description: A dataset containing 1811 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ruellia asperula"
 ]
}

 The dataset includes 1811 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036330-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zw2zw3
title: Occurrence Download

description: A dataset containing 71 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.continent = 'NORTH_AMERICA'
 AND (occurrence.decimallatitude &gt;= 21.2603 AND occurrence.decimallatitude &lt;= 51.70066 AND (occurrence.decimallongitude &gt;= -128.29868 AND occurrence.decimallongitude &lt;= -55.79363) AND GBIF_WITHIN('POLYGON ((-128.29868 21.2603, -67.40962 21.2603, -58.70012 42.89228, -55.79363 49.73616, -67.40962 51.70066, -128.29868 51.70066, -128.29868 21.2603))', occurrence.decimallatitude, occurrence.decimallongitude) = TRUE)
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (CAST(occurrence.taxonkey AS INTEGER) = 2480566 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 2480566 OR CAST(occurrence.kingdomkey AS INTEGER) = 2480566 OR CAST(occurrence.phylumkey AS INTEGER) = 2480566 OR CAST(occurrence.classkey AS INTEGER) = 2480566 OR CAST(occurrence.orderkey AS INTEGER) = 2480566 OR CAST(occurrence.familykey AS INTEGER) = 2480566 OR CAST(occurrence.genuskey AS INTEGER) = 2480566 OR CAST(occurrence.specieskey AS INTEGER) = 2480566)
 AND (occurrence."year" &gt;= 1950 AND occurrence."year" &lt;= 2020)
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 71 records were derived from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036291-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/9q64g-z7r67
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/dga2017-03-16-5/rawdata/</p>DeltaVirB7_Cc_20170316a0009.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/dga2017-03-16-5/rawdata/DeltaVirB7_Cc_20170316a0009.mrc"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316a0009_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/dga2017-03-16-5/3dimage_109148/DeltaVirB7_Cc_20170316a0009_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316a0009.ali,  392.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-16-5/file_25869/DeltaVirB7_Cc_20170316a0009.ali"
        > <i class="download icon"></i> Download </a></p>

        DeltaVirB7_Cc_20170316a0009.tlt,  440.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-16-5/file_25872/DeltaVirB7_Cc_20170316a0009.tlt"
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        DeltaVirB7_Cc_20170316a0009_fid.tlt,  440.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.rmrgd6
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036333-250811113504898/datasets/export for details.
DOI: 10.22002/5423s-z4w50
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/dga2017-10-27-19/rawdata/</p>Xan_CaulDelT1_20172710g0007.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/dga2017-10-27-19/rawdata/Xan_CaulDelT1_20172710g0007.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172710g0007_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xan_CaulDelT1_20172710g0007.ali,  356.4 MB  
        
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        Xan_CaulDelT1_20172710g0007.tlt,  400.0 B  
        
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        Xan_CaulDelT1_20172710g0007_fid.tlt,  400.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/5kbxm-ant45
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/dga2017-03-08-9/rawdata/</p>Xac_wt_20170308_V4_tgt00010006.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xac_wt_20170308_V4_tgt00010006_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xac_wt_20170308_V4_tgt00010006.ali,  506.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xac_wt_20170308_V4_tgt00010006.tlt,  568.0 B  
        
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        Xac_wt_20170308_V4_tgt00010006_fid.tlt,  568.0 B  
        
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DOI: 10.22002/ghmt8-6a878
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>
  dga2016-11-04-101_slicer17248.jpg: OM invagination for possible injection to nearby cells dga2016-11-04-101_slicer17249.jpg: OM invagination for possible injection to nearby cells dga2016-11-04-101_slicer17250.jpg: chemoreceptor arrays or cytoskeleton-like filaments?
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-101/rawdata/</p>15D_Pos4_atlas20072.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/dga2016-11-04-101/rawdata/15D_Pos4_atlas20072.mrc"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20072_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20072.ali,  570.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20072.tlt,  640.0 B  
        
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        15D_Pos4_atlas20072_fid.tlt,  640.0 B  
        
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