cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/epzaq-5as16
title: Coxiella burnetii_wt_D15

description: Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-15  culture.
description: <strong>Tilt Series Date:</strong> 2016-11-04</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 130.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab</p>
  dga2016-11-04-59_slicer17253.jpg: Membrane remodeling?
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-59/rawdata/</p>15D_Pos4_atlas20030.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-59/rawdata/15D_Pos4_atlas20030.mrc"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20030_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-59/3dimage_108177/15D_Pos4_atlas20030_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20030.ali,  577.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-59/file_24659/15D_Pos4_atlas20030.ali"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20030.tlt,  648.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-59/file_24660/15D_Pos4_atlas20030.tlt"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20030_fid.tlt,  648.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ttq6vt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Teredo navalis",
 "Country is Russian Federation",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032950-250811113504898/datasets/export for details.
DOI: 10.15468/dl.qjyhh6
title: Occurrence Download

description: A dataset containing 13399 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "TaxonKey is Papilio zelicaon"
 ]
}

 The dataset includes 13399 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032949-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/nvs5t-r5646
title: Coxiella burnetii_wt_D15

description: Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-15  culture.
description: <strong>Tilt Series Date:</strong> 2016-11-04</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 130.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab</p>
  dga2016-11-04-38_slicer17261.jpg: poration of membrane vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-38/rawdata/</p>15D_Pos4_atlas20009.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-38/rawdata/15D_Pos4_atlas20009.mrc"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20009_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20009.ali,  577.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-11-04-38/file_24605/15D_Pos4_atlas20009.ali"
        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20009.tlt,  648.0 B  
        
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        > <i class="download icon"></i> Download </a></p>

        15D_Pos4_atlas20009_fid.tlt,  648.0 B  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.zmn8zh
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhabdalestes tangensis)",
 "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 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032951-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7267/vh53x498p
title: Supplemental Data: Listeria monocytogenes Growth Dynamics in Hispanic-Style Cheeses

description: This dataset contains supplemental materials associated with the study “Behavior of Listeria monocytogenes in commercial queso fresco and queso cotija and investigation of salt concentration as a control factor.” The supplemental tables provide growth curve parameters of L. monocytogenes in queso fresco across manufacturers and production lots, as well as results of linear mixed-effects models evaluating the impact of storage duration and remaining shelf life on growth outcomes. The supplemental figure presents inoculation data and fitted mechanistic growth models for L. monocytogenes in queso cotija products from multiple manufacturers during refrigerated storage at 7°C for 28 days. Together, these files provide parameter estimates, statistical outputs, and visualizations that document microbial behavior in Hispanic-style cheeses under defined experimental conditions.
DOI: 10.22002/0877r-ywd12
title: Mega gas vesicles

description: Mega gas vesicles, purified, -1 to -5 micron defocus. Reconstruct with included scripts for ctf-corrected bin1 tomogram.
description: <strong>Tilt Series Date:</strong> 2019-09-25</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Bacillus megaterium</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-39.0°, 39.0°), step: 3°, constant angular increment, dosage: 70.0 eV/Å²,  defocus: 0.0 μm,  magnification: 81000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD 4.9.8, ctffind4, custom scripts</p>
<strong>Collaborators and Roles:</strong> purified by Rob Hurt and George Lu from the Shapiro lab at Caltech; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas with assistance from Przemek Dutka</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified Mega gas vesicles in 10 mM HEPES</p>
<strong>Sample Preparation:</strong> protochips C-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-2/rawdata/</p>01_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-2/rawdata/01_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        01_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 442.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-2/3dimage_121806/01_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_01.mrc.mdoc,  28.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-2/rawdata/TS_01.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-2/file_27684/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 21.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-2/file_27685/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/n9pk7-g5b67
title: H. Neapolitanus Carboxysomes

description: Carboxysomes purified from H. Neapolitanus, WT, high resolution
description: <strong>Tilt Series Date:</strong> 2019-08-21</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Halothiobacillus neapolitanus</p>
<strong>Strain:</strong> c2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: 0.0 μm,  magnification: 81000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD, ctffind4, novaCTF, custom bash and Matlab scripts</p>
<strong>Collaborators and Roles:</strong> purified by Tom Laughlin in the Savage lab at Berkeley; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified by the Savage lab</p>
<strong>Sample Preparation:</strong> protochip C-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity, defocus varying -1 to -5.5 microns</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-55/rawdata/</p>55_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 4.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-55/rawdata/55_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        55_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 479.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-55/3dimage_113121/55_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_55.mrc.mdoc,  30.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-55/rawdata/TS_55.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-55/file_26722/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 13.6 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-55/file_26723/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7ya04-w7y97
title: Shewanella OMV delMTR

description: Shewanella outer membrane vesicles, delMTR (cytochromes) knockout, high resolution
description: <strong>Tilt Series Date:</strong> 2018-09-12</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</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: 0.0 μm,  magnification: 82000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD, ctffind4, custom scripts</p>
<strong>Collaborators and Roles:</strong> purified by Lori Zacharoff in the El Naggar lab at USC; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas</p>
<strong>Sample Preparation:</strong> C-Flat 2/2-300 mesh grid, 10nm BSA-gold, 100% humidity, -1.5 to -5 micron defocus</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-12/rawdata/</p>29_dose-filt.st,  Tilt Series (Pixel Size 0.1778 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-12/rawdata/29_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        29_dose-filt.rec,  Reconstruction (Pixel Size 0.7112 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-12/3dimage_102938/29_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_29.mrc.mdoc,  24.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-12/rawdata/TS_29.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 2.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-12/file_20313/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 7.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-12/file_20314/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/sar3p-czs96
title: Shewanella OMV delMTR delDMSOR

description: Shewanella outer membrane vesicles, delMTR, del DMSO Reductase, high resolution
description: <strong>Tilt Series Date:</strong> 2018-09-14</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</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: 0.0 μm,  magnification: 82000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD, ctffind4, custom scripts</p>
<strong>Collaborators and Roles:</strong> purified by Lori Zacharoff in the El Naggar lab at USC; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas</p>
<strong>Sample Preparation:</strong> protochip c-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity, -1.5 to -5 micron defocus</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-14-2/rawdata/</p>02_dose-filt.st,  Tilt Series (Pixel Size 0.1778 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-14-2/rawdata/02_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        02_dose-filt.rec,  Reconstruction (Pixel Size 0.7112 nm), 81.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-14-2/3dimage_103116/02_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_02.mrc.mdoc,  24.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-14-2/rawdata/TS_02.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 2.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-14-2/file_20361/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 5.6 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-14-2/file_20362/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/r6skv-kmb23
title: H. Neapolitanus Carboxysomes

description: Carboxysomes purified from H. Neapolitanus, WT, high resolution
description: <strong>Tilt Series Date:</strong> 2019-08-21</p>
<strong>Data Taken By:</strong> LaurenAnn Metskas</p>
<strong>Species / Specimen:</strong> Halothiobacillus neapolitanus</p>
<strong>Strain:</strong> c2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: 0.0 μm,  magnification: 81000x. </p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> IMOD, ctffind4, novaCTF, custom bash and Matlab scripts</p>
<strong>Collaborators and Roles:</strong> purified by Tom Laughlin in the Savage lab at Berkeley; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas</p>
<strong>Purification / Growth Conditions / Treatment:</strong> purified by the Savage lab</p>
<strong>Sample Preparation:</strong> protochip C-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity, defocus varying -1 to -5.5 microns</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-1/rawdata/</p>01_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 3.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-1/rawdata/01_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        01_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 479.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-1/3dimage_113013/01_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 12.7 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-1/file_26561/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-1/file_26560/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        TS_01.mrc.mdoc,  30.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-1/rawdata/TS_01.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>