cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/m6y9r-y8k61
title: Drp1

description: Drp1
description: <strong>Tilt Series Date:</strong> 2013-01-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Drp1</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> David Chan</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-01-01-52/rawdata/</p>drp1_275_8defocus0038.mrc,  Tilt Series (Pixel Size 0.4 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/576-zpx-rmk
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gq2-x9s-8rl
title: Phyllolepidum Trinajstic

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/k3f53-19922
title: Agrobacterium tumefaciens

description: C58 wild type
description: <strong>Tilt Series Date:</strong> 2013-08-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</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: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 19500x. </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> Pat Zambyski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> induced for T-pili with 300mM AS</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-08-01-60/rawdata/</p>c58_au_300uM0013.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/4ft-1pa-jdq
title: Monodon Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/vb38g-ea126
title: Sulfolobus solfac.P2

description: Sulfolobus solfactaricus P2 cells- active culture fixed with 0.5% glutiraldehyde.
description: <strong>Tilt Series Date:</strong> 2014-02-20</p>
<strong>Data Taken By:</strong> Rasika Ramdasi</p>
<strong>Species / Specimen:</strong> Sulfolobus solfataricus </p>
<strong>Strain:</strong> P2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 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> with Jamie Snyder from Montana</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Active culture fixed</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-27/rawdata/</p>atlas20023.mrc,  Tilt Series (Pixel Size 0.48 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/rra2014-02-20-27/rawdata/atlas20023.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.6fcyqm
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gobio carpathicus)",
 "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 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012074-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5bvet3
title: Occurrence Download

description: A dataset containing 1452 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mycobacterium ulcerans"
 ]
}

 The dataset includes 1452 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012075-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/3tffn-4rs12
title: Streptococcus pneumoniae

description: deletion strain
description: <strong>Tilt Series Date:</strong> 2013-09-16</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Streptococcus pneumoniae</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: 200.0 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> Andrew Camilli</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-09-16-8/rawdata/</p>strep_delta0004.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xkr5b-wkj04
title: Streptomyces venezuelae

description: Raw data files of Streptomyces venezuelae
description: <strong>Tilt Series Date:</strong> 2012-11-18</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Streptomyces venezuelae</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 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> Justin Nodwell gave the cells</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells were clumping</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-11-18-2/rawdata/</p>Svenecuelae0002.mrc,  Tilt Series (Pixel Size 0.5 nm), 3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-11-18-2/rawdata/Svenecuelae0002.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.tzxtnq
title: Occurrence Download

description: A dataset containing 1452 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mycobacterium ulcerans"
 ]
}

 The dataset includes 1452 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012077-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/lzr-ryf-xsk
title: Bourgueticrinina Sieverts-Doreck, 1953

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.9aa34c
title: Occurrence Download

description: A dataset containing 2454 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus setaceus",
 "Country is Spain",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2454 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012076-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ydej6-a8d77
title: Agrobacterium tumefaciens

description: Agrobacterium_Bald_strain
description: <strong>Tilt Series Date:</strong> 2013-06-01</p>
<strong>Data Taken By:</strong> Elitza Tocheva</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°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from Pat Zambryski</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-01-3/rawdata/</p>agrobald10012.mrc,  Tilt Series (Pixel Size 0.48 nm), 2.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-01-3/rawdata/agrobald10012.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1r4ra-dyj25
title: Agrobacterium tumefaciens

description: wild type C58
description: <strong>Tilt Series Date:</strong> 2013-06-27</p>
<strong>Data Taken By:</strong> Elitza Tocheva</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: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </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> Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> wild type induced with AS for T-pili synthesis</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-06-27-2/rawdata/</p>c580003.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/etl2013-06-27-2/rawdata/c580003.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/h2g0g-cja47
title: Vibrio cholerae SAD2095 induced

description: SAD2095 (T2SS and T4 competence pili) = rpoS*, pilA S81C, lacZ::lacIq, comEA-mCherry, ΔluxO, Ptac-tfoX, Ptac-recA, ∆TCP::ZeoR, ∆MSHA::CarbR, ∆CTX::KanR, ∆pilT::TmRAnkur: "For the taxonomy ID - unfortunately the strain we sent does not have a taxonomy ID. So, you can use the generic one for V. cholerae which is "666". The strain we are working with is related to N16961, but is certainly not the same strain, so not sure if you would want to indicate that somehow? Just for reference - the strain we sent is E7946 (although it is obviously heavily modified with a number of mutations). "
description: <strong>Tilt Series Date:</strong> 2018-08-13</p>
<strong>Data Taken By:</strong> Sara Weaver</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> SAD2095</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 0.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, data collected by Sara Weaver</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Streaked stock on a plate. Grew up a single colony in 3 mL LB with shaking at 37˚C. The next day, subcultured 416 uL of this overnight culture into 25 mL of fresh LB+100uM IPTG + 20mM MgCl2 + 10mM CaCl2 in a 125 mL beveled glass flask and grow at 30˚C shaking for ~6 hours.</p>
<strong>Sample Preparation:</strong> Grid SW0808A2 - Spun gold (100 µL 10 nm gold + 25 µL 5% BSA) at 15,000rpm for 20 minutes, removed supernatant. Resuspended gold beads in 20 µL liquid culture. Vitrobot RT and 95% humidity, vortex sample immediately before taking 4 µL of gold/sample slurry on carbon/copper Quantifoil Finder grids R2/2 (EmiTech glow discharge 20 mA, 60 s) Blot force +6, blot time 3 s, no waiting time, no drain time. Plunged into ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-08-13-25/rawdata/</p>0808A2_tomo33.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        0808A2_tomo33_full.rec,  Reconstruction (Pixel Size 1.56 nm), 711.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/b7r-45d-36g
title: Eucidaris tribuloides (Lamarck, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/axp2w-kz386
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/mka2019-10-28-48/rawdata/</p>Hpylori_FliM_050_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_050_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: 10.22002/8m77w-dgs70
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> 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 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/mka2019-09-21-9/rawdata/</p>Hpylori_dFliO7.mrc,  Tilt Series (Pixel Size 0.4494 nm), 2.4 GB  
        
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        Hpylori_dFliO7.mrc.mdoc,  28.0 kB  
        
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DOI: 10.22002/9p0xr-znm41
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/mka2019-11-19-165/rawdata/</p>Hpylori_dfliQ_165_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_165_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>