cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/11gv3-szn87
title: O. tauri @ G1

description: O. tauri cell synchronization .
description: <strong>Tilt Series Date:</strong> 2007-09-27</p>
<strong>Data Taken By:</strong> Lu Gan</p>
<strong>Species / Specimen:</strong> Ostreococcus tauri</p>
<strong>Strain:</strong> RCC745</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> prepared by Lu Gan at Caltech; data collected by Lu Gan; processed by Lu Gan</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Treated with HU for 12h, then PP for 3h, then fresh MK</p>
<strong>Sample Preparation:</strong> Q-foil R3.5/1, BSA treated 10nm gold, 100% humidity, -2mm offset,</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2007-09-27-30/rawdata/</p>RCC745_HUPP_3h_8AM_03.mrc,  Tilt Series (Pixel Size 1.26 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2007-09-27-30/rawdata/RCC745_HUPP_3h_8AM_03.mrc"
        > <i class="download icon"></i> Download </a></p>

        RCC745_HUPP_3h_8AM_03.rec,  Reconstruction (Pixel Size 2.52 nm), 345.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.3qnkam
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Yucca aloifolia",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 120 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047785-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/848dn-xp894
title: Sacculus

description: C. crescentus CB15N sacculus .
description: <strong>Tilt Series Date:</strong> 2006-10-15</p>
<strong>Data Taken By:</strong> Lu Gan</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -4.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> prepared by Lu Gan at Caltech; data collected by Lu Gan; processed by Lu Gan</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown to exponential phase in PYE; Purified by hot SDS</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1, BSA treated 10nm gold, 100% humidity, -2mm offset,</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-10-15-1/rawdata/</p>Ghost01.mrc,  Tilt Series (Pixel Size 0.56 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-10-15-1/rawdata/Ghost01.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ghost01.rec,  Reconstruction (Pixel Size 0.56 nm), 239.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-10-15-1/3dimage_3008/Ghost01.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.7910/dvn/tnt3fv
title: Modeling

description: For ghrelin modeling
DOI: 10.22002/y3836-8g314
title: Pdj 122708 634

description: Prosthecobacter dejongeii, 08dec28a_Pdj_739_w2_023,
description: <strong>Tilt Series Date:</strong> 2008-12-28</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-28-16/rawdata/</p>08dec28a_Pdj_739_w2_023.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-28-16/rawdata/08dec28a_Pdj_739_w2_023.mrc"
        > <i class="download icon"></i> Download </a></p>

        08dec28a_Pdj_739_w2_023_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/2r7tv-st713
title: Target8

description: Dead spore. Stacks in spore, structures in mother cell.Keywords: DNA stacks
description: <strong>Tilt Series Date:</strong> 2008-04-28</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Strain:</strong> None</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: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Eric Matson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Anaerobic growth on CO2+Glu</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2008-04-28-10/rawdata/</p>target8.mrc,  Tilt Series (Pixel Size 0.961 nm), 771.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2008-04-28-10/rawdata/target8.mrc"
        > <i class="download icon"></i> Download </a></p>

        target8_full.rec,  Reconstruction (Pixel Size 1.922 nm), 677.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2008-04-28-10/3dimage_2205/target8_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.5ndg7h
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Yucca aloifolia",
 "Country is Seychelles",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047784-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/mss61-r3508
title: Agrobacterium tumefaciens C1

description: Wild type, no T4SS
description: <strong>Tilt Series Date:</strong> 2014-02-01</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: 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> liquid LB</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-39/rawdata/</p>c1_70002.mrc,  Tilt Series (Pixel Size 0.4 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-39/rawdata/c1_70002.mrc"
        > <i class="download icon"></i> Download </a></p>

        c1_70002.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/etl2014-02-01-39/3dimage_49230/c1_70002.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.4ecpf5
title: Occurrence Download

description: A dataset containing 367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Asclepias angustifolia"
 ]
}

 The dataset includes 367 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047787-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x5g3bg
title: Occurrence Download

description: A dataset containing 600 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Denmark",
 "Geometry POLYGON((8.16398 56.67847,8.35995 56.71408,8.43659 56.75612,8.60519 56.89512,8.7 57.14732,8.55921 57.13069,8.34754 57.0636,8.16398 56.67847))",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EX, EW, CR, EN, VU, NT, LC, DD, NE)",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset includes 600 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047788-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.37ukb3
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047786-250811113504898/datasets/export for details.
DOI: 10.5281/zenodo.16954301
title: Model-based Error Grids and Satellite-derived errors for the World Magnetic Model (WMM)

description: 1) The first part (*.mat) of the dataset contains the final processed error grids and global altitude profiles for the World Magnetic Model (WMM) as presented in the manuscript "Global geomagnetic model errors as a function of altitude and geomagnetic activity." The errors, combining both omission and commission sources, were calculated on a 3D grid (10∘×10∘ latitude/longitude) at 29 discrete altitude levels from the Earth's surface to 10,000 km. The dataset is binned by five levels of geomagnetic activity (G0-G4). These results were generated by synthesizing outputs from established models for the crustal (EMM), ionospheric (AMPS, DIFI), and magnetospheric (T89) fields. The data are provided in MATLAB .mat file format, with variables corresponding to each activity level and magnetic field component. 

2) The second part (*.txt) of the dataset provides processed root-mean-square (RMS) errors of the World Magnetic Model (WMM) derived from satellite observations, used for validation in the manuscript "Global geomagnetic model errors as a function of altitude and geomagnetic activity." The data are sourced from the CHAMP, Swarm A, Swarm B, and CryoSat-2 satellite missions spanning 2005-2024. The processing methodology includes subtracting the relevant WMM version, binning the residuals by geomagnetic activity level (G0-G4), removing outliers, and correcting for secular variation (SV) forecast error using the CHAOS-8.2 model. The final data are provided as a set of ASCII text files, with values corresponding to the validation markers presented in Figure 5 of the associated publication.
DOI: 10.5281/zenodo.16954302
title: Model-based Error Grids and Satellite-derived errors for the World Magnetic Model (WMM)

description: 1) The first part (*.mat) of the dataset contains the final processed error grids and global altitude profiles for the World Magnetic Model (WMM) as presented in the manuscript "Global geomagnetic model errors as a function of altitude and geomagnetic activity." The errors, combining both omission and commission sources, were calculated on a 3D grid (10∘×10∘ latitude/longitude) at 29 discrete altitude levels from the Earth's surface to 10,000 km. The dataset is binned by five levels of geomagnetic activity (G0-G4). These results were generated by synthesizing outputs from established models for the crustal (EMM), ionospheric (AMPS, DIFI), and magnetospheric (T89) fields. The data are provided in MATLAB .mat file format, with variables corresponding to each activity level and magnetic field component. 

2) The second part (*.txt) of the dataset provides processed root-mean-square (RMS) errors of the World Magnetic Model (WMM) derived from satellite observations, used for validation in the manuscript "Global geomagnetic model errors as a function of altitude and geomagnetic activity." The data are sourced from the CHAMP, Swarm A, Swarm B, and CryoSat-2 satellite missions spanning 2005-2024. The processing methodology includes subtracting the relevant WMM version, binning the residuals by geomagnetic activity level (G0-G4), removing outliers, and correcting for secular variation (SV) forecast error using the CHAOS-8.2 model. The final data are provided as a set of ASCII text files, with values corresponding to the validation markers presented in Figure 5 of the associated publication.
DOI: 10.22002/1mg1e-mwq69
title: Pdb 122308 396

description: Prosthecobacter debontii, 08dec25b_pdj_002,
description: <strong>Tilt Series Date:</strong> 2008-12-25</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter debontii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-25-1/rawdata/</p>08dec25b_pdj_002.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-25-1/rawdata/08dec25b_pdj_002.mrc"
        > <i class="download icon"></i> Download </a></p>

        08dec25b_pdj_002_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2008-12-25-1/3dimage_13364/08dec25b_pdj_002_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ts094-xqw81
title: Hyphomonas session5 27KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2008-11-18</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2008-11-18-37/rawdata/</p>08nov18a_b620_1_043.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2008-11-18-37/rawdata/08nov18a_b620_1_043.mrc"
        > <i class="download icon"></i> Download </a></p>

        08nov18a_b620_1_043_1k.rec,  Reconstruction (Pixel Size 1.548 nm), 80.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/hm8rm-r0337
title: Hyphomonas session4 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2008-11-01</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2008-11-01-56/rawdata/</p>08nov01a_b17x1_056.mrc,  Tilt Series (Pixel Size 0.632 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        08nov01a_b17x1_056_1k.rec,  Reconstruction (Pixel Size 1.26 nm), 176.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/tcgsw-awe68
title: Mesoplasma florum

description: Mesoplasma florum, dual axis 2, total dose 60 e/A2
description: <strong>Tilt Series Date:</strong> 2004-04-14</p>
<strong>Data Taken By:</strong> Elizabeth Wright</p>
<strong>Species / Specimen:</strong> Mesoplasma florum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Dual Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 60.0 eV/Å²,  defocus: 15.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> N/A</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Overnight culture in Mycoplasma media</p>
<strong>Sample Preparation:</strong> R2/2 quantifoil, 10 nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ewr2004-04-14-2/rawdata/</p>60mfb_n2_side1_041404.mrc,  Tilt Series (Pixel Size 6.7 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        60mfb_n2_side2_041404.mrc,  Tilt Series (Pixel Size 6.7 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/5a0df-gzq32
title: Mesoplasma florum dual axis

description: Mesoplasma florum, dual axis, total dose 110 e/A2 - 2
description: <strong>Tilt Series Date:</strong> 2005-02-18</p>
<strong>Data Taken By:</strong> Elizabeth Wright</p>
<strong>Species / Specimen:</strong> Mesoplasma florum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Dual Axis, tilt range: (-70.0°, 70.0°), step: 1°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: 10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> N/A</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Overnight culture in Mycoplasma media</p>
<strong>Sample Preparation:</strong> R2/2 quantifoil, 10 nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ewr2005-02-18-2/rawdata/</p>c2_22k_10_p5.mrc,  Tilt Series (Pixel Size 0.961 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        c2_22k_10_p6.mrc,  Tilt Series (Pixel Size 0.961 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>