cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/13e51-62t95
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/dga2017-04-27-39/rawdata/</p>Xac-mini-20170427w10003.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/dga2017-04-27-39/rawdata/Xac-mini-20170427w10003.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427w10003_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/dga2017-04-27-39/3dimage_109249/Xac-mini-20170427w10003_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427w10003.ali,  498.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-39/file_26244/Xac-mini-20170427w10003.ali"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170427w10003.tlt,  560.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-39/file_26245/Xac-mini-20170427w10003.tlt"
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        Xac-mini-20170427w10003_fid.tlt,  560.0 B  
        
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DOI: 10.22002/1t838-r9t40
title: JV7967

description: Legionella thyA ΔdotI ΔdotJ
description: <strong>Tilt Series Date:</strong> 2016-08-11</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</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 Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV7967 strain at OD~3.3. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-48/rawdata/</p>JV79670025.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-48/rawdata/JV79670025.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV79670025_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/dga2016-08-11-48/3dimage_108438/JV79670025_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        JV79670025.tlt,  648.0 B  
        
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        > <i class="download icon"></i> Download </a></p>

        T2SSK.mod,  1.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-48/file_25214/T2SSK.mod"
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        T2SSK_2k.mod,  1.0 kB  
        
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DOI: 10.22002/k16xg-7qr15
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/dga2017-10-21-27/rawdata/</p>Xan_CaulDelT1_20172110b0002.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/dga2017-10-21-27/rawdata/Xan_CaulDelT1_20172110b0002.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110b0002_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/dga2017-10-21-27/3dimage_108741/Xan_CaulDelT1_20172110b0002_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xan_CaulDelT1_20172110b0002.ali,  335.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-27/file_25654/Xan_CaulDelT1_20172110b0002.ali"
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        Xan_CaulDelT1_20172110b0002.tlt,  376.0 B  
        
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        Xan_CaulDelT1_20172110b0002_fid.tlt,  376.0 B  
        
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DOI: 10.22002/ea81a-75d39
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/dga2017-04-27-15/rawdata/</p>Xac-mini-20170426b0004.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/dga2017-04-27-15/rawdata/Xac-mini-20170426b0004.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170426b0004_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/dga2017-04-27-15/3dimage_109211/Xac-mini-20170426b0004_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170426b0004.ali,  506.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-15/file_26090/Xac-mini-20170426b0004.ali"
        > <i class="download icon"></i> Download </a></p>

        Xac-mini-20170426b0004.tlt,  568.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-15/file_26091/Xac-mini-20170426b0004.tlt"
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        Xac-mini-20170426b0004_fid.tlt,  568.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-15/file_26092/Xac-mini-20170426b0004_fid.tlt"
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DOI: 10.22002/74qd7-4sp11
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/dga2017-10-21-6/rawdata/</p>Xan_CaulDelT1_201721100005.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/dga2017-10-21-6/rawdata/Xan_CaulDelT1_201721100005.mrc"
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        Xan_CaulDelT1_201721100005_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xan_CaulDelT1_201721100005.ali,  434.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-10-21-6/file_25681/Xan_CaulDelT1_201721100005.ali"
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        Xan_CaulDelT1_201721100005.tlt,  488.0 B  
        
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        Xan_CaulDelT1_201721100005_fid.tlt,  488.0 B  
        
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DOI: 10.22002/f0as3-nx387
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/dga2017-04-27-13/rawdata/</p>Xac-mini-20170426b0002.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/dga2017-04-27-13/rawdata/Xac-mini-20170426b0002.mrc"
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        Xac-mini-20170426b0002_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        Xac-mini-20170426b0002.ali,  506.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-04-27-13/file_26084/Xac-mini-20170426b0002.ali"
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        Xac-mini-20170426b0002.tlt,  568.0 B  
        
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        Xac-mini-20170426b0002_fid.tlt,  568.0 B  
        
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DOI: 10.22002/3qb34-qzr07
title: pl_scale5

description: Raw data files of pl_scale5
description: <strong>Tilt Series Date:</strong> 2020-11-09</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Allium cepa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Onion peels generated like Kafle et al. 2013, incubated in HEPES >20min until freezing</p>
<strong>Sample Preparation:</strong> Glow-discharged (15mA – 1min) Quantifoil R2/2 NH2 Cu EM grids (EMSdiasum). Plunge freezing was performed with a 60/40 ratio ethane/propane mix and an FEI Vitrobot Mark IV (Thermo Fisher). Humidity was set at 50%, temperature at 20°C. Grids were first manually backblotted for 6 s in order to attach the cell wall peel firmly to the carbon, followed by two autoblottings (front and back) 5 s, maximal blot force (25) and a drain time of 3 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-14/rawdata/</p>on29-2_lam5_ts1.mrc,  Tilt Series (Pixel Size 0.33 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-14/rawdata/on29-2_lam5_ts1.mrc"
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        on29-2_lam5_ts1_rec.hdf,  Reconstruction (Pixel Size 1.32 nm), 1.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        postprocess_masked_on29.mrc,  Reconstruction (Pixel Size 0.67 nm) Average done by Przchemek, 257.0 kB  
        
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        on29-2_lam5_ts1.rawtlt,  240.0 B  
        
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        on29-2_lam5_ts1.mrc.mdoc,  17.6 kB  
        
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