cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/we694-mqw14
title: Agro_AD1484

description: Agro_AD1484 (AD1484:A348dB/pAD2079,virB on a multicopy plasmid). Add 200 ul of induction media to one of the induction plate (containing lawn of Agrobacterium AD1484) and wash the plate by gently rolling the liquid. Take this liquid and add to the other plate. Repeat the same. This should get enough cells dissolved in the liquid.Add gold to this: 1ul of gold to 4 ul of cells.
description: <strong>Tilt Series Date:</strong> 2015-10-06</p>
<strong>Data Taken By:</strong> Debnath Ghosal</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: 160.0 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</p>
<strong>Collaborators and Roles:</strong> Strain constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow AD1484 cells on AB solid medium with Cb (pH 7) at 30C. For induction, use one single colony and spread on induction plates (AB Mes pH 5.8) containing Cb (50ug/ml)+AS (200µM). Grow at 19C for 4days. Add 200 ul of induction media to one of the induction plate (containing lawn of Agrobacterium AD1484) and wash the plate by gently rolling the liquid. Add gold to this: 1ul of gold to 4 ul of cells, freeze.</p>
<strong>Sample Preparation:</strong> 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.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-06-6/3dimage_69982/</p>AD1584_B1tgt0005_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/dga2015-10-06-6/3dimage_69982/AD1584_B1tgt0005_full.rec"
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        AD1584_B1tgt0005.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/dga2015-10-06-6/rawdata/AD1584_B1tgt0005.mrc"
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DOI: 10.22002/n7xyt-j3648
title: Agro_AD1484

description: Agro_AD1484 (AD1484:A348dB/pAD2079,virB on a multicopy plasmid).Cb resistance. Grown on induction plate pH5.8
description: <strong>Tilt Series Date:</strong> 2015-10-26</p>
<strong>Data Taken By:</strong> Debnath Ghosal</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: 1.5°, constant angular increment, dosage: 160.0 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</p>
<strong>Collaborators and Roles:</strong> Strain constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Agro_AD1484 (AD1484:A348dB/pAD2079,virB on a multicopy plasmid). Cells were scraped off the induction plate (particularly from the immediate surface of the plate: this is to ensure that if something is happening on the real surface of the plate, we do not miss it), dissolved in induction media, spun for 15 min in a table top centrifuge, supernatant thrown away, cells redissolved in PBS. Add gold to this: 1ul of gold to 4 ul of cells and freeze.</p>
<strong>Sample Preparation:</strong> 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.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-26-46/3dimage_70918/</p>20151026_AD1484_20026_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
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        20151026_AD1484_20026.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/dga2015-10-26-46/rawdata/20151026_AD1484_20026.mrc"
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DOI: 10.22002/aras5-16395
title: JV5443

description: JV5443 Legionella (Super-deletion+CDHFG), no Thy
description: <strong>Tilt Series Date:</strong> 2016-08-09</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 Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate and cysteine hydrochloride  (no 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 JV5443 strain at OD~3.2. 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/dga2016-08-09-43/rawdata/</p>JV5443a0010.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/dga2016-08-09-43/rawdata/JV5443a0010.mrc"
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        JV5443a0010_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/dga2016-08-09-43/3dimage_77660/JV5443a0010_full.rec"
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DOI: 10.22002/e7b4h-q6k09
title: JV7091

description: JV7091 is a double mutant that lacks dotE and dotP (Lp02).Cell density was quite low on the grid!
description: <strong>Tilt Series Date:</strong> 2016-01-12</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. 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> 6 grids were frozen for the JV7091 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/dga2016-01-12-56/3dimage_72581/</p>7091_area_atlas11_100010011.rec,  Reconstruction (Pixel Size 1.68 nm), 861.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-12-56/3dimage_72581/7091_area_atlas11_100010011.rec"
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        7091_area_atlas11_100010011.mrc,  Tilt Series (Pixel Size 0.42 nm), 1.8 GB  
        
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DOI: 10.22002/xqf9q-48p18
title: JV1644 Legionella thyA ΔdotO

description: JV1644 Legionella thyA ΔdotO. Lacks dotO ATPase.
description: <strong>Tilt Series Date:</strong> 2016-06-14</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: 1.5°, constant angular increment, dosage: 120.0 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> 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.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV1644 strain 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 ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-06-14-119/rawdata/</p>JV1644_150620164th0042.mrc,  Tilt Series (Pixel Size 3.9 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-06-14-119/rawdata/JV1644_150620164th0042.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV1644_150620164th0042.rec,  Reconstruction (Pixel Size 15.6 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-06-14-119/3dimage_75810/JV1644_150620164th0042.rec"
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DOI: 10.22002/dzah2-x3094
title: JV918 Legionella thyA ΔdotB

description: Legionella thyA ΔdotB. Lacks dotB ATPase.
description: <strong>Tilt Series Date:</strong> 2017-08-08</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: 2°, constant angular increment, dosage: 100.0 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> 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 ~2.6.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for this strain 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/dga2017-08-08-77/rawdata/</p>20170808_JV918b0080.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/dga2017-08-08-77/rawdata/20170808_JV918b0080.mrc"
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        20170808_JV918b0080_part61_7.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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DOI: 10.22002/dwahm-cne19
title: JV1180_ΔdotUF

description: Legionella thyA ΔdotUF (JV1180). JV1180 is an independent isolate of the UF deletion. JV1180 and JV1181 are same thing.
description: <strong>Tilt Series Date:</strong> 2017-08-16</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: -7.0 μm,  magnification: 27500x. </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</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.</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 it was ~2.4.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4 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/dga2017-08-16-69/rawdata/</p>20170814_JV1180a0068.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/dga2017-08-16-69/rawdata/20170814_JV1180a0068.mrc"
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        20170814_JV1180a0068_part61_2.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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DOI: 10.22002/br16k-y0260
title: FtsZ structure at dividing site

description: ingle tilt. Constant angular increment. FtsZ. Complete ring. Caulobacter.
description: <strong>Tilt Series Date:</strong> 2015-03-10</p>
<strong>Data Taken By:</strong> Qing Yao</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: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFtomo</p>
<strong>Purification / Growth Conditions / Treatment:</strong> C. crescentus was from Yi-Wei's cryo-stock and was grown in PYE medium overnight at 30°c 250 rpm. In the next days' morning, 1/20 subculture into the M2G medium. When OD600 reaches 0.48, 1ml medium was spun down and the resuspension was 100 ul for cryo-grid preparation.</p>
<strong>Sample Preparation:</strong> Glow discharged Quantifoil R2/R holey carbon film. 4 ul concentrated gold suspension was added to 16 ul bacteria and mix before plunge freezing. Plunge freezing condition: 6(force)-2(duration time)-1(dry time). Tilt Series Setting: single tilt. constant angular increment, step: 1. tilt range: (-60, 60). dosage: 120/A2. defocus: -10um. magnification: 22500.</p>
  qya2015-03-10-3_slicer12815.jpg: Invagination from the outer curvature side qya2015-03-10-3_slicer12816.jpg: FtsZ ring appears complete on the left side and incomplete on the right side. qya2015-03-10-3_slicer13006.jpg: Invagination qya2015-03-10-3_slicer13007.jpg: FtsZ on both sides
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2015-03-10-3/rawdata/</p>Qing15_10003.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2015-03-10-3/rawdata/Qing15_10003.mrc"
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        Qing15_10003_part121_1.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2015-03-10-3/3dimage_53025/Qing15_10003_part121_1.rec"
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DOI: 10.22002/qxjgq-dfa31
title: JV1644 Legionella thyA ΔdotO

description: JV1644 Legionella thyA ΔdotO. Lacks dotO ATPase.
description: <strong>Tilt Series Date:</strong> 2016-06-14</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: 1.5°, constant angular increment, dosage: 120.0 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> 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.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV1644 strain 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/dga2016-06-14-7/rawdata/</p>DG1644_150620160007.mrc,  Tilt Series (Pixel Size 3.9 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-06-14-7/rawdata/DG1644_150620160007.mrc"
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        DG1644_150620160007.rec,  Reconstruction (Pixel Size 15.6 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-06-14-7/3dimage_75594/DG1644_150620160007.rec"
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