cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/dd17g-hkd23
title: Pseudomonas aerugionsa PA103

description: This strain was obtained from Alan Hauser's lab from Northwestern University. It contains a plasmid containing the FtsZ gene. The over-expression of FtsZ will produce minicells. Other than the plasmid, this strain is the same as the wild type.
description: <strong>Tilt Series Date:</strong> 2019-06-19</p>
<strong>Data Taken By:</strong> Steven Wang</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</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: 95.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Jensen Lab tomography pipeline (RAPTOR for alignment)</p>
<strong>Collaborators and Roles:</strong> Alan Hauser lab from Northwestern University</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were grown in LB with 50 ug/mL gentamicin. Incubate the cells for 1 hour at 37 C 200 rpm at a dilution factor of  50. Then add IPTG to reach a final concentration of 1 mM. Incubate for 6 hours at 37 C at 200 rpm. Then remove most of the filamentous cells by 3000xg centrifugation for 10 min. Collect the minicells from the supernatant with another centrifugation at 15,000xg for 30 min.</p>
<strong>Sample Preparation:</strong> Mix 40 uL of cells with gold beads concentrated from 200 uL Au solution + 50 uL 5% BSA. Plunge freeze the samples with liquid ethane and propane with a blotting force of 4, a blotting time of 3 s or 4s and a draining time of 1 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-06-19-4/rawdata/</p>Pa_cell_target_13.mrc,  Tilt Series (Pixel Size 0.45 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-06-19-4/rawdata/Pa_cell_target_13.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pa_cell_target_13_part44_1.rec,  Reconstruction (Pixel Size 1.8 nm), 589.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swy2019-06-19-4/3dimage_103980/Pa_cell_target_13_part44_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/q273t-exr31
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/mka2019-10-28-150/rawdata/</p>Hpylori_FliM_152_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/mka2019-10-28-150/rawdata/Hpylori_FliM_152_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_152_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/mka2019-10-28-150/3dimage_107953/Hpylori_FliM_152_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.jazfet
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum notatum",
 "Country is El Salvador",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013637-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8ms6hh
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Creagrutus peruanus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013636-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/g97gh-2b385
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/mka2019-09-21-57/rawdata/</p>Hpylori_dFliO12_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/mka2019-09-21-57/rawdata/Hpylori_dFliO12_Good.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dFliO12_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/mka2019-09-21-57/3dimage_106760/Hpylori_dFliO12_Good_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6zb6w-jw562
title: H_pylori_dFliO_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliO mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-25</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 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/mka2019-10-25-157/rawdata/</p>Hpylori_FliO_160_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/mka2019-10-25-157/rawdata/Hpylori_FliO_160_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_160_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/mka2019-10-25-157/3dimage_107551/Hpylori_FliO_160_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/k0gvb-yp747
title: Ecoli_EPEC_8612

description: Bacterial nanotubes as described by the work of Ilan Rosenshine and Sigal Ben Yehuda labs at  .  the Hebrew university).
description: <strong>Tilt Series Date:</strong> 2020-02-14</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: 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> 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/mka2020-02-14-133/rawdata/</p>EPEC_8612_239_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/mka2020-02-14-133/rawdata/EPEC_8612_239_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_239_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/mka2020-02-14-133/3dimage_111284/EPEC_8612_239_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.zsdzfp
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum notatum",
 "Country is Eswatini",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013638-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/3sffe-g0071
title: Ecoli_EPEC_8612

description: Bacterial nanotubes as described by the work of Ilan Rosenshine and Sigal Ben Yehuda labs at  .  the Hebrew university).
description: <strong>Tilt Series Date:</strong> 2020-02-14</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: 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> 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/mka2020-02-14-69/rawdata/</p>EPEC_8612_146_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/mka2020-02-14-69/rawdata/EPEC_8612_146_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_146_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/mka2020-02-14-69/3dimage_111179/EPEC_8612_146_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.a7ubbu
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013639-250827131500795/datasets/export for details.
DOI: 10.22002/w4f2h-enr55
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/mka2019-11-19-103/rawdata/</p>Hpylori_dfliQ_103_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/mka2019-11-19-103/rawdata/Hpylori_dfliQ_103_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_103_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9n6yt-asx56
title: Helicobacter_Pylori_dFlgs

description: These are H. pylori cells that don't have a complete FliP. In addition, FlgS 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> 2019-09-22</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> None</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 FlgS 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/mka2019-09-22-25/rawdata/</p>Hpylori_dFlgS20.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/mka2019-09-22-25/rawdata/Hpylori_dFlgS20.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dFlgS20.mrc.mdoc,  28.1 kB  
        
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        > <i class="download icon"></i> Download </a></p>