cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/m2ea7-7g015
title: E_coli_EPEC_8612

description: The aim is to look for bacterial nanotubes (See Pal et al., 2019 Cell)
description: <strong>Tilt Series Date:</strong> 2020-02-13</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 105.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> These cells were obtained from Ritesh (Ilan Rosenshine lab) and Amit (Sigal ben Yehuda lab, . both from the Hebrew university). They were present during sample preparation.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> An overnight culture from -80C stock was made in 2ml LB and was grown at 37C in static . conditions. The next day, 1 ml of cells were spun down at 4000 rpm for six minutes and . concentrated 10 times. 3 ul of cells were spotted on glow-discharged grids located on a . DMEM high-glucose agar plates (1.5% agar) for 3 hours. Then, the grids were washed twice . in PBS and transferred to a starvation-medium agar plates (Starvation medium:DMEM without . phenol red, vitamins and amino acids). and incubated for 1 hour at 37C. Subsequently,the . samples were washed with PBS and plunge-frozen. </p>
<strong>Sample Preparation:</strong> The samples were hold with a tweezer from the starvation plates and washed with PBS. Blotted . with different conditions (B</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-13-100/rawdata/</p>EPEC_8612_050_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-13-100/rawdata/EPEC_8612_050_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_050_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-13-100/3dimage_111002/EPEC_8612_050_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/m395r-e0d93
title: Hpylori_dfliG

description: These are H. pylori cells that don't have a complete FliP. In addition, FliG was knocked out in  .  these cells. The aim is to study the assembly of the flagellar motor and the core complex.
description: <strong>Tilt Series Date:</strong> 2019-11-23</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP protein. Therefore, they don't assemble full . flagella. We knocked out FliG protein of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1. 100% humidity. Cu grids. 10 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-23-37/rawdata/</p>Hpylori_dfliG_030_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-23-37/rawdata/Hpylori_dfliG_030_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliG_030_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-23-37/3dimage_109395/Hpylori_dfliG_030_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/rn99y-1en15
title: Hpylori_dfliQ

description: These are fast tilt series taken on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-11-19</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP protein. Therefore, they don't . assemble full flagella. We knocked out FliQ protein of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. The cells were grown for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids . were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot, time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. . 10 nm gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-179/rawdata/</p>Hpylori_dfliQ_179_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-179/rawdata/Hpylori_dfliQ_179_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_179_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-179/3dimage_109041/Hpylori_dfliQ_179_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/c4r56-k6m60
title: Helicobacter_Pylori_dFliO

description: These are H. pylori cells that don't have a complete FliP. In addition, FliO was knocked out in  .  these cells. The aim is to study the assembly of the flagellar motor and the core complex.
description: <strong>Tilt Series Date:</strong> 2019-09-21</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild . type cells but they don't express complete FliP protein. Therefore, they don't assemble full . flagella. We knocked out FliO protein of the flagellar motor to study the early assembly . . states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1. 100% humidity. Cu grids. 10 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-21-75/rawdata/</p>Hpylori_dFliO40_good.mrc,  Tilt Series (Pixel Size 0.4494 nm), 2.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-21-75/rawdata/Hpylori_dFliO40_good.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dFliO40_good_full.rec,  Reconstruction (Pixel Size 1.7976 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-21-75/3dimage_106777/Hpylori_dFliO40_good_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7n90k-mt675
title: H-pylori_dFliM_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they . don't express complete FliP protein. Therefore, they don't assemble full flagella. We knocked out FliM protein . of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. 10 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-172/rawdata/</p>Hpylori_FliM_174_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-172/rawdata/Hpylori_FliM_174_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_174_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-172/3dimage_108000/Hpylori_FliM_174_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.edk5zu
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "TaxonKey is Mucuna globulifera"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013562-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/gss76-98347
title: Hpylori_dfliQ

description: These are fast tilt series taken on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-11-19</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP protein. Therefore, they don't . assemble full flagella. We knocked out FliQ protein of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. The cells were grown for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids . were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot, time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. . 10 nm gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-114/rawdata/</p>Hpylori_dfliQ_114_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-114/rawdata/Hpylori_dfliQ_114_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_114_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-114/3dimage_108924/Hpylori_dfliQ_114_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.a7fbby
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis strigosa",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 307 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013563-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/t1szz-ch681
title: JV7091_ΔdotEP

description: JV7091_ΔdotEP (Deletion of dotE and dotP)
description: <strong>Tilt Series Date:</strong> 2017-09-05</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 ~2.8</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for this strain at OD~ 2.8, cell density was increased to 2x by centrifugation. 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/dga2017-09-05-36/rawdata/</p>JV7091_20170906a0014.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/dga2017-09-05-36/rawdata/JV7091_20170906a0014.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV7091_20170906a0014_full.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/dga2017-09-05-36/3dimage_88221/JV7091_20170906a0014_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.sgug7h
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapholis strigosa",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013564-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xzwxmv
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013565-250827131500795/datasets/export for details.
DOI: 10.22002/gajmr-h6q94
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/dga2017-08-16-5/rawdata/</p>20170814_JV1180a0004.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/dga2017-08-16-5/rawdata/20170814_JV1180a0004.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170814_JV1180a0004_full.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/dga2017-08-16-5/3dimage_87719/20170814_JV1180a0004_full.rec"
        > <i class="download icon"></i> Download </a></p>