cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15482/usda.adc/29646779.v1
title: Validation Dataset for Hydroponically Cultivated Bibb Lettuce

description: This dataset supplements the existing dataset "Hydroponic Cultivation of Bibb Lettuce in Nitrogen Phosphorus Potassium (NPK)-Limited Conditions" (https://doi.org/10.15482/USDA.ADC/28801286.v1). To use, replace the prior "NPK.CrossT.All" spreadsheet with this updated version.This comprehensive dataset includes a variety of data types, data volumes, true replications, and pseudo replications of data collected as time-series data during the entire lifecycle for hydroponic lettuce cultivation experiments. This dataset contains large amounts of elemental analysis far beyond anything published previously in part for potential use in future research. Bibb lettuce (Lactuca sativa) was grown in vertical farm-wall style hydroponic systems, in controlled environment chambers at 21.5 Celsius and 50-70% relative humidity, and in multiple limiting nutrient conditions for Nitrogen, Phosphorus, and Potassium. For an additional level of in-depth detail, see methodology in referenced manuscript(s).The prior dataset includes 18 files, while this validation dataset includes 3 novel files (plus an updated version of the CrossT file). The base files (everything except CrossT) contain identical formatting, a significant amount of preliminary fundamental interpretation/manipulation (e.g., dividing "dry mass" by "fresh mass" to get "dry mass %"), and multiple worksheets (tabs) which summarize data on other worksheets. Anytime there is ambiguity or lack-of-understanding on what a cell means, it may be helpful to highlight a data cell in that column to see which other columns/cells it references and follow the chain of references. The final file is the workbook "NPK.CrossT.All" which references and summarizes all other workbooks in the dataset, and is useful for easy reference when analyzing data across all tabs.
DOI: 10.22002/p2j1n-j8a76
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/lma2019-08-21-3/rawdata/</p>03_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/lma2019-08-21-3/rawdata/03_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        03_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-3/3dimage_113017/03_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 14.7 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-3/file_26567/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-3/file_26566/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        TS_03.mrc.mdoc,  30.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-3/rawdata/TS_03.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6stq2-vq498
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/lma2019-08-21-18/3dimage_113047/</p>18_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 516.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-18/3dimage_113047/18_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        18_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/lma2019-08-21-18/rawdata/18_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 14.7 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-18/file_26612/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-18/file_26611/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        TS_18.mrc.mdoc,  30.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-18/rawdata/TS_18.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/zmm8z-kwd30
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/lma2018-09-12-8/rawdata/</p>24_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/lma2018-09-12-8/rawdata/24_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        24_dose-filt.rec,  Reconstruction (Pixel Size 0.7112 nm), 86.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-8/3dimage_102896/24_dose-filt.rec"
        > <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/lma2018-09-12-8/file_20301/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        TS_24.mrc.mdoc,  24.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-8/rawdata/TS_24.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 9.5 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-8/file_20302/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.mynhws
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Teredo navalis",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 19 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032954-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/f2gy2-vh358
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/lma2019-09-25-10/rawdata/</p>09_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 2.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-10/rawdata/09_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        09_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 331.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-10/3dimage_121822/09_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_09.mrc.mdoc,  28.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-10/rawdata/TS_09.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-10/file_27708/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 22.8 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-10/file_27709/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.qt4bey
title: Occurrence Download

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

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032955-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/h11z3-ngh31
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/lma2019-08-21-40/rawdata/</p>40_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 4.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-40/rawdata/40_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        40_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 405.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-40/3dimage_113091/40_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_40.mrc.mdoc,  30.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-40/rawdata/TS_40.mrc.mdoc"
        > <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/lma2019-08-21-40/file_26677/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 12.5 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-08-21-40/file_26678/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/agryj-qqw95
title: Mega gas vesicles

description: Mega gas vesicles, purified from E. coli, -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: (-48.0°, 51.0°), 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/lma2019-09-25-30/rawdata/</p>30_dose-filt.st,  Tilt Series (Pixel Size 0.1104 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-30/rawdata/30_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        30_dose-filt.rec,  Reconstruction (Pixel Size 0.8832 nm), 368.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-30/3dimage_121861/30_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_30.mrc.mdoc,  28.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-30/rawdata/TS_30.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/lma2019-09-25-30/file_27768/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 25.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2019-09-25-30/file_27769/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3yzy5-cyd40
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/lma2018-09-12-24/rawdata/</p>43_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/lma2018-09-12-24/rawdata/43_dose-filt.st"
        > <i class="download icon"></i> Download </a></p>

        43_dose-filt.rec,  Reconstruction (Pixel Size 0.7112 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-24/3dimage_103065/43_dose-filt.rec"
        > <i class="download icon"></i> Download </a></p>

        TS_43.mrc.mdoc,  24.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-24/rawdata/TS_43.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>

        frames.tar.bz2,  zipped raw frames, 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-24/file_20349/frames.tar.bz2"
        > <i class="download icon"></i> Download </a></p>

        scripts.tar.bz2,  zipped processing scripts, 8.5 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lma2018-09-12-24/file_20350/scripts.tar.bz2"
        > <i class="download icon"></i> Download </a></p>