cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/4gxfs-tbj10
title: JV4404_delDot.Icm_Lp02

description: JV4404 is deletion of the Dot.Icm system. 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
description: <strong>Tilt Series Date:</strong> 2015-12-11</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: (-50.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: -8.0 μm,  magnification: 22500x. </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, also manually processed 12 tomograms (and used SIRT) to check for presence of the T4SS basal-body</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. This data was collected at the Caltech Polara.</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. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for JV4404 at OD= 2.9 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/dga2015-12-11-22/3dimage_71362/</p>JV44040021_part111_3.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-12-11-22/3dimage_71362/JV44040021_part111_3.rec"
        > <i class="download icon"></i> Download </a></p>

        JV44040021.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-12-11-22/rawdata/JV44040021.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/b99ew-68y24
title: JV9082

description: DotF-sfGFP fusion to the wild-type gene on the chromosome (thyA).
description: <strong>Tilt Series Date:</strong> 2017-07-06</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: 2°, 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> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</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. 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. This time cell density was 2.7</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. 3 grids with extra-thick carbon (JV9082T) and three finder grids (JV9082F). 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/dga2017-07-06-225/rawdata/</p>atlas-area1-20170706-JV9082tomo0056.mrc,  Tilt Series (Pixel Size 0.42 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-06-225/rawdata/atlas-area1-20170706-JV9082tomo0056.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas-area1-20170706-JV9082tomo0056_part61_2.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-06-225/3dimage_86668/atlas-area1-20170706-JV9082tomo0056_part61_2.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/z5m2d-4be54
title: JV4404_delDot.Icm_Lp02

description: JV4404 is deletion of the Dot.Icm system. 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
description: <strong>Tilt Series Date:</strong> 2015-12-11</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: (-50.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: -8.0 μm,  magnification: 22500x. </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, also manually processed 12 tomograms (and used SIRT) to check for presence of the T4SS basal-body</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. This data was collected at the Caltech Polara.</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. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for JV4404 at OD= 2.9 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/dga2015-12-11-39/3dimage_71395/</p>JV4404atlas20002_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-12-11-39/3dimage_71395/JV4404atlas20002_full.rec"
        > <i class="download icon"></i> Download </a></p>

        JV4404atlas20002.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/dga2015-12-11-39/rawdata/JV4404atlas20002.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/16gdq-d7385
title: Lp02_Legionella pneumophila

description: Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. 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
description: <strong>Tilt Series Date:</strong> 2015-10-29</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: 1.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor, also manually processed 25 tomograms (and used SIRT)for subtomogram averaging.</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. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. 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. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for Lp02 at OD= 2.8 and another 4 grids for Lp02 at OD= 3.3Vitrobot (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/dga2015-10-29-60/3dimage_70758/</p>20151029_LP02_10060_part121_3.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-29-60/3dimage_70758/20151029_LP02_10060_part121_3.rec"
        > <i class="download icon"></i> Download </a></p>

        20151029_LP02_10060.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-29-60/rawdata/20151029_LP02_10060.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gm5t7-1qv15
title: Lp02_Legionella pneumophila

description: Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. 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
description: <strong>Tilt Series Date:</strong> 2015-10-29</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: 1.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor, also manually processed 25 tomograms (and used SIRT)for subtomogram averaging.</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. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. 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. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for Lp02 at OD= 2.8 and another 4 grids for Lp02 at OD= 3.3Vitrobot (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/dga2015-10-29-21/3dimage_70677/</p>20151029_LP02_10037_part121_17.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-29-21/3dimage_70677/20151029_LP02_10037_part121_17.rec"
        > <i class="download icon"></i> Download </a></p>

        20151029_LP02_10037.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-29-21/rawdata/20151029_LP02_10037.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/af3qg-xmp02
title: JV3559_Janelia

description: Legionella thyA ΔdotG.This is a single mutant that lacks DotG.
description: <strong>Tilt Series Date:</strong> 2017-01-08</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> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</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 F30, Caltech.</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. This time cell density was ~3.4</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV3559 strain at OD~ 3.4, 4 grids at density x and another 4 at density 2x. 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/dga2017-01-08-50/3dimage_80371/</p>JV3559_20170106_area10066_full.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-01-08-50/3dimage_80371/JV3559_20170106_area10066_full.rec"
        > <i class="download icon"></i> Download </a></p>

        JV3559_20170106_area10066.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/dga2017-01-08-50/rawdata/JV3559_20170106_area10066.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/d4tbs-1wf96
title: Lp02_2nd

description: 2nd time collection: Jan 2016. Defocus -6.Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. 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
description: <strong>Tilt Series Date:</strong> 2016-01-15</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> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</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. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. 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. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> Grids were stored in Janelia from previous imaging. See previous Lp02 sample prep. 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/dga2016-01-15-84/rawdata/</p>atlas_area_a0009.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-84/rawdata/atlas_area_a0009.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas_area_a0009_part81_2.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-84/3dimage_72951/atlas_area_a0009_part81_2.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.17011793
title: AG-WaMED PRIMA Project dataset

description: This is the public database of the AG-WaMED PRIMA Project (https://agwamed.eu/)

AG-WaMED is funded by the Partnership for Research and Innovation in the Mediterranean Area Programme (PRIMA), an Art.185 initiative supported and funded under Horizon 2020, the European Union’s Framework Programme for Research and Innovation.

Grant Agreement Number No. [Italy: 391 del 20/10/2022, Egypt: 45878, Tunisia: 0005874-004-18-2022-3, Greece: ΓΓP21-0474657, Spain: PCI2022-132929, Algeria: N° 04/PRIMA_section 2/2021 ]The content of the database reflects the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein.
DOI: 10.5281/zenodo.17011794
title: AG-WaMED PRIMA Project dataset

description: This is the public database of the AG-WaMED PRIMA Project (https://agwamed.eu/)

AG-WaMED is funded by the Partnership for Research and Innovation in the Mediterranean Area Programme (PRIMA), an Art.185 initiative supported and funded under Horizon 2020, the European Union’s Framework Programme for Research and Innovation.

Grant Agreement Number No. [Italy: 391 del 20/10/2022, Egypt: 45878, Tunisia: 0005874-004-18-2022-3, Greece: ΓΓP21-0474657, Spain: PCI2022-132929, Algeria: N° 04/PRIMA_section 2/2021 ]The content of the database reflects the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein.