cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/5zw34-g6n16
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 https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-30-98/rawdata/</p>Xac_Cc_20170329b0041.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/dga2017-03-30-98/rawdata/Xac_Cc_20170329b0041.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170329b0041_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_20170329b0041.ali,  491.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170329b0041.tlt,  552.0 B  
        
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        Xac_Cc_20170329b0041_fid.tlt,  552.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.7tm4k5
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Acaena magellanica"
 ]
}

 The dataset includes 155 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033020-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/dfvs3-qyk13
title: Mega gas vesicles

description: Mega gas vesicles, purified, -1 to -5 micron defocus. Reconstruct with included scripts for ctf-corrected bin1 tomogram.
description: <strong>Tilt Series Date:</strong> 2019-09-25</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Bacillus megaterium</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-39.0°, 39.0°), step: 3°, constant angular increment, dosage: 70.0 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 4.9.8, ctffind4, custom scripts</p>
<strong>Collaborators and Roles:</strong> purified by Rob Hurt and George Lu from the Shapiro lab at Caltech; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas with assistance from Przemek Dutka</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified Mega gas vesicles in 10 mM HEPES</p>
<strong>Sample Preparation:</strong> protochips C-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-9/rawdata/</p>08_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 2.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-9/rawdata/08_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        08_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 294.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-9/3dimage_121820/08_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_08.mrc.mdoc,  28.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-9/rawdata/TS_08.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-9/file_27705/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 19.5 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-9/file_27706/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qt05n-qt768
title: Wild type control

description: Raw data files of Wild type control
description: <strong>Tilt Series Date:</strong> 2009-08-01</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, PEACH</p>
<strong>Collaborators and Roles:</strong> Experiments were done by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase NA1000 cells.</p>
<strong>Sample Preparation:</strong> 10 nm gold </p>
  zla2009-08-01-14_slicer4293.jpg: S-layer zla2009-08-01-14_slicer4294.jpg: Unknown filament zla2009-08-01-14_slicer4295.jpg: Granule
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-14/rawdata/</p>09aug01a_noaddctl1_014.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-14/rawdata/09aug01a_noaddctl1_014.mrc"
        > <i class="download icon"></i> Download </a></p>

        09aug01a_noaddctl1_014_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        zl2009-08-01-14_clip01.rec,  Reconstruction (Pixel Size 2.4 nm) cropped by Sarah, 66.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        zl2009-08-01-14_clip01-label-Filament01.am,  filament segmented by Sarah, 1.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-14/file_3080/zl2009-08-01-14_clip01-label-Filament01.am"
        > <i class="download icon"></i> Download </a></p>

        zl2009-08-01-14_clip01-label-Filament02.am,  filament segmented by Sarah, 1.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/wmzw1-ne628
title: AimB depletion w/ Glucose

description: filament segmented by Sarah
description: <strong>Tilt Series Date:</strong> 2009-07-30</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> The AimB depletion strain was constructed by John Werner in Zemer Gitai's lab. Depletion was done by Zhuo Li. Data were collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The AimB depletion strain was depleted serially with 0.2% glucose. </p>
<strong>Sample Preparation:</strong> 10 nm</p>
  zla2009-07-30-20_slicer4879.jpg: Unknown filaments zla2009-07-30-20_slicer4880.jpg: Unknown
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-20/rawdata/</p>09jul30a_AimBglu_020.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-20/rawdata/09jul30a_AimBglu_020.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jul30a_AimBglu_020_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        zl2009-07-30-20_clip01.rec,  Reconstruction (Pixel Size 2.4 nm) cropped by Sarah, 70.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-20/3dimage_13120/zl2009-07-30-20_clip01.rec"
        > <i class="download icon"></i> Download </a></p>

        zl2009-07-30-20_clip01-label_Filament01.am,  filament segmented by Sarah, 1.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-20/file_3078/zl2009-07-30-20_clip01-label_Filament01.am"
        > <i class="download icon"></i> Download </a></p>

        zl2009-07-30-20_clip01-label_Filament02.am,  filament segmented by Sarah, 1.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/hvc84-zb394
title: Agrobacterium C58 25C plate liq

description: C58 wild type
description: <strong>Tilt Series Date:</strong> 2014-05-30</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</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: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </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> IMOD</p>
<strong>Collaborators and Roles:</strong> Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown at 25 on plates for 2 days then recovered in liquid for 5 h</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
  etl2014-05-30-15_slicer6240.jpg: filament etl2014-05-30-15_slicer6241.jpg: filament etl2014-05-30-15_slicer6243.jpg: flat vesicle etl2014-05-30-15_slicer6244.jpg: filament etl2014-05-30-15_slicer6245.jpg: pilli etl2014-05-30-15_slicer6248.jpg: pilli .  filament etl2014-05-30-15_slicer9044.jpg: flat vesicles connected to the membrane .  Agrobacterium .  snapshot by Megan
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-05-30-15/rawdata/</p>c58_25_pl_liq0008.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-05-30-15/rawdata/c58_25_pl_liq0008.mrc"
        > <i class="download icon"></i> Download </a></p>

        c58_25_pl_liq0008_full.rec,  Reconstruction (Pixel Size 0.0 nm), 833.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        slicer000.tif,  2.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-05-30-15/file_11751/slicer000.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer001.tif,  2.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-05-30-15/file_11752/slicer001.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer002.tif,  2.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-05-30-15/file_11753/slicer002.tif"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/tjcb5-r5382
title: AimB depletion w/ Glucose

description: Raw data files of AimB depletion w/ Glucose
description: <strong>Tilt Series Date:</strong> 2009-07-30</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> The AimB depletion strain was constructed by John Werner in Zemer Gitai's lab. Depletion was done by Zhuo Li. Data were collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The AimB depletion strain was depleted serially with 0.2% glucose. </p>
<strong>Sample Preparation:</strong> 10 nm</p>
  zla2009-07-30-10_slicer4869.jpg: Intracellular flat vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-10/rawdata/</p>09jul30a_AimBglu_010.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-10/rawdata/09jul30a_AimBglu_010.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jul30a_AimBglu_010_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        zl2009-07-30-10_clip01.rec,  Reconstruction (Pixel Size 2.4 nm) cropped by Sarah, 73.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        zl2009-07-30-10_clip01-label-Filament01.am,  filament segmented by Sarah, 1.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-10/file_3076/zl2009-07-30-10_clip01-label-Filament01.am"
        > <i class="download icon"></i> Download </a></p>

        zl2009-07-30-10_clip01-label-Filament02.am,  filament segmented by Sarah, 1.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/95cbs-wrz11
title: Sulfolobus cells synchronized for division

description: search for ESCRT in dividing cells
description: <strong>Tilt Series Date:</strong> 2011-01-16</p>
<strong>Data Taken By:</strong> Megan Dobro</p>
<strong>Species / Specimen:</strong> Sulfolobus acidocaldarius</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 1.5 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> grown and synchronized by Rachel Samson in Stephen Bell's lab, Oxford University</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in Brock's Medium at 80C, synchronize with Baby Machine</p>
<strong>Sample Preparation:</strong> frozen at Kay Grunewald's lab. Harrick plasma cleaner. Blotted on one sides, 6 sec, sponge for humidity</p>
  mdj2011-01-16-6_slicer8733.jpg: OMV .  Sulfolobus acidocaldarius mdj2011-01-16-6_slicer8735.jpg: pili .  Sulfolobus acidocaldarius mdj2011-01-16-6_slicer8738.jpg: pili .  Sulfolobus acidocaldarius
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-01-16-6/rawdata/</p>11jan16a_Bx13gr2_006.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-01-16-6/rawdata/11jan16a_Bx13gr2_006.mrc"
        > <i class="download icon"></i> Download </a></p>

        11jan16a_Bx13gr2_006_full.rec,  Reconstruction (Pixel Size 2.5 nm), 922.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11jan16a_Bx13gr2_006.rec,  Reconstruction (Pixel Size 2.5 nm), 142.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-01-16-6/3dimage_19320/11jan16a_Bx13gr2_006.rec"
        > <i class="download icon"></i> Download </a></p>

        11jan16a_Bx13gr2_006mode1.rec,  Reconstruction (Pixel Size 2.5 nm), 284.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11jan16a_Bx13gr2_006median.rec,  Reconstruction (Pixel Size 2.5 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2011-01-16-6/3dimage_19322/11jan16a_Bx13gr2_006median.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3s65b-f1n38
title: V. cholerae delta CheA1,2,3

description: Vibrio cholerae strain deleted for CheA1, CheA2, and CheA3
description: <strong>Tilt Series Date:</strong> 2014-05-05</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O1 biovar El Tor</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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> Raptor</p>
<strong>Collaborators and Roles:</strong> Ikuro Kawagishi</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grew in LB 24 hours at 30C; diluted 150 µL into 2 mL Ca-HEPES buffer and grew 16 hours at 30C</p>
  aba2014-05-05-13_slicer3872.jpg: chemoreceptor array in delta Chea1,2,3 strain aba2014-05-05-13_slicer3873.jpg: chemoreceptor array in delta Chea1,2,3 strain aba2014-05-05-13_slicer3874.jpg: chemoreceptor array in delta Chea1,2,3 strain
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-05-05-13/rawdata/</p>VibrioDelta123May0013.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
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        VibrioDelta123May0013.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        VibrioDelta123May0013SIRT.rec,  Reconstruction (Pixel Size 0.0 nm), 4.4 GB  
        
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        VibrioDelta123May0013SIRTrot.rec,  Reconstruction (Pixel Size 0.0 nm), 4.4 GB  
        
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        VibrioDelta123May0013SIRTrotmedian.rec,  Reconstruction (Pixel Size 0.0 nm), 4.4 GB  
        
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