cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/zneg5-kxp67
title: Bsubtilis349

description: Bsubtilis JFG349 (MJ007, SpoIIIE78-11-GFP)
description: <strong>Tilt Series Date:</strong> 2011-08-24</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> JFG349, ponA null, SpoIIIE73-11-GFP</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 Kit Pogliano at UCSD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation media</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/etl2011-08-24-3/3dimage_24937/</p>349target0007_full.rec,  Reconstruction (Pixel Size 1.9 nm), 706.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-08-24-3/3dimage_24937/349target0007_full.rec"
        > <i class="download icon"></i> Download </a></p>

        349target0007.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/etl2011-08-24-3/rawdata/349target0007.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/c1q78-yy180
title: A22-treated wild type

description: Raw data files of A22-treated wild type
description: <strong>Tilt Series Date:</strong> 2009-07-26</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR Peach</p>
<strong>Collaborators and Roles:</strong> Cell culture and treatment by Zhuo Li. Data collected by Zhuo Li. Processed by Zhuo Li. </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponentially growing NA1000 cells were treated with 10 ug/ml A22 for 2 hours before freezing. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-26-34/rawdata/</p>09jul26c_A22wt_034.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-26-34/rawdata/09jul26c_A22wt_034.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jul26c_A22wt_034_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/rn6ct-t1k35
title: Hyphomonas chq session19 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-06-25</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: (-61.0°, 61.0°), step: 2°, constant angular increment, dosage: 75.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </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 Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, chloroquine 1.0mg/ml, 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-25-46/rawdata/</p>09jun25a_bx217d_100.mrc,  Tilt Series (Pixel Size 0.632 nm), 536.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun25a_bx217d_100_full.rec,  Reconstruction (Pixel Size 1.264 nm), 419.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-25-46/3dimage_8157/09jun25a_bx217d_100_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/z01rq-xax72
title: Hyphomonas session7 41KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-02-05</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: (-63.0°, 63.0°), step: 1.5°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -5.0 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>
  jsa2009-02-05-30_slicer9236.jpg: Hyphomonas neptunium  .  ring
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-02-05-30/rawdata/</p>09feb05a_Hm7I_039.mrc,  Tilt Series (Pixel Size 0.512 nm), 704.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09feb05a_Hm7I_039_1k.rec,  Reconstruction (Pixel Size 1.024 nm), 60.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/28yav-vy366
title: Ote 090409 MP22

description: Opitutus terrae, 09sep10b_090409MP22_039,
description: <strong>Tilt Series Date:</strong> 2009-09-10</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Opitutus terrae</p>
<strong>Strain:</strong> DSM 11246</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/mpa2009-09-10-70/rawdata/</p>09sep10b_090409MP22_039.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/mpa2009-09-10-70/rawdata/09sep10b_090409MP22_039.mrc"
        > <i class="download icon"></i> Download </a></p>

        09sep10b_090409MP22_039_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xmvt0-h1e48
title: Pva 032409 609

description: Prosthecobacter vanneervenii, 09apr01a_Pvashake609_014, putative btub structure (1 tube),
description: <strong>Tilt Series Date:</strong> 2009-04-01</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter vanneervenii</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 ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-04-01-8/rawdata/</p>09apr01a_Pvashake609_014.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/mpa2009-04-01-8/rawdata/09apr01a_Pvashake609_014.mrc"
        > <i class="download icon"></i> Download </a></p>

        09apr01a_Pvashake609_014_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-04-01-8/3dimage_13764/09apr01a_Pvashake609_014_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/m56d2-nbp14
title: Eco 041010 MP56

description: Escherichia coli, 10apr19a_042010_MP56_041,
description: <strong>Tilt Series Date:</strong> 2010-04-19</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 19.1 Martin</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/mpa2010-04-19-8/rawdata/</p>10apr19a_042010_MP56_041.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/mpa2010-04-19-8/rawdata/10apr19a_042010_MP56_041.mrc"
        > <i class="download icon"></i> Download </a></p>

        10apr19a_042010_MP56_041_part.rec,  Reconstruction (Pixel Size 1.9 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/crjbt-a1529
title: Pdj 122708 634

description: Prosthecobacter dejongeii, 09jan04b_pdj_624w1_005, filaments,
description: <strong>Tilt Series Date:</strong> 2009-01-04</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/mpa2009-01-04-4/rawdata/</p>09jan04b_pdj_624w1_005.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jan04b_pdj_624w1_005_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1rw3t-49b56
title: Hyphomonas EB session21 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-07-14</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: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </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 Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, EB 0.02mg/ml overnight 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-26/rawdata/</p>09jul14a_b200c_026.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul14a_b200c_026_full.rec,  Reconstruction (Pixel Size 1.264 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5522/04/29939663
title: Co<sup>2+</sup> mediated adsorption facilitates atomic force microscopy of DNA molecules at double-helix resolution

description: Atomic force microscopy (AFM) has demonstrated the ability to resolve single DNA molecules in liquid at a spatial resolution that is sufficient to visualize the double helix structure and variations therein. Such variations can be due to inherent configurational flexibility and may be related to, e.g., DNA sequence, ionic screening, supercoiling, or protein binding. These AFM experiments require DNA to be adhered to a solid and preferably flat support. For high-resolution, in-liquid AFM studies so far, such adhesion has commonly been achieved using Ni<sup>2+</sup> ions to electrostatically bridge between the negatively charged DNA and a negatively charged, atomically flat mica surface, yet Ni<sup>2+</sup> ions tend to cause precipitation of salts on the surface, increasing the risk of AFM tip contamination and increasing the corrugation of the support surface, making it harder to distinguish secondary DNA structure.Here, we provide the dataset that underpins a study on sample preparation protocol that, instead, relies on Co<sup>2+</sup> ions to adhere DNA to mica. While the Co<sup>2+</sup> is similarly effective as Ni<sup>2+</sup> for facilitating DNA adsorption onto mica, it leads to significantly reduced salt precipitation with the potential to provide enhanced reproducibility in high-resolution DNA imaging by AFM. We expect this to substantially facilitate high-resolution AFM studies of DNA in aqueous solutions.The data are in the form of AFM files that can be opened, e.g., by open-source software as available at https://gwyddion.net/, and numerical values in xlsx format for the quantification of the images.These data belong to a study Pailing et al., accepted for publication in Nanoscale and available as a preprint at https://www.biorxiv.org/content/10.1101/2025.05.29.655787v1.
DOI: 10.5522/04/29939663.v1
title: Co<sup>2+</sup> mediated adsorption facilitates atomic force microscopy of DNA molecules at double-helix resolution

description: Atomic force microscopy (AFM) has demonstrated the ability to resolve single DNA molecules in liquid at a spatial resolution that is sufficient to visualize the double helix structure and variations therein. Such variations can be due to inherent configurational flexibility and may be related to, e.g., DNA sequence, ionic screening, supercoiling, or protein binding. These AFM experiments require DNA to be adhered to a solid and preferably flat support. For high-resolution, in-liquid AFM studies so far, such adhesion has commonly been achieved using Ni<sup>2+</sup> ions to electrostatically bridge between the negatively charged DNA and a negatively charged, atomically flat mica surface, yet Ni<sup>2+</sup> ions tend to cause precipitation of salts on the surface, increasing the risk of AFM tip contamination and increasing the corrugation of the support surface, making it harder to distinguish secondary DNA structure.Here, we provide the dataset that underpins a study on sample preparation protocol that, instead, relies on Co<sup>2+</sup> ions to adhere DNA to mica. While the Co<sup>2+</sup> is similarly effective as Ni<sup>2+</sup> for facilitating DNA adsorption onto mica, it leads to significantly reduced salt precipitation with the potential to provide enhanced reproducibility in high-resolution DNA imaging by AFM. We expect this to substantially facilitate high-resolution AFM studies of DNA in aqueous solutions.The data are in the form of AFM files that can be opened, e.g., by open-source software as available at https://gwyddion.net/, and numerical values in xlsx format for the quantification of the images.These data belong to a study Pailing et al., accepted for publication in Nanoscale and available as a preprint at https://www.biorxiv.org/content/10.1101/2025.05.29.655787v1.
DOI: 10.22002/2bqc4-ap428
title: MT310_xyl(-)_metal(-)

description: Raw data files of MT310_xyl(-)_metal(-)
description: <strong>Tilt Series Date:</strong> 2009-06-21</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</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: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> The MT310 strain was constructed by Martin Thanbichler; cell cultured and treated by Zhuo Li; data collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> MT310 cells were cultured for 20 hours. No xylsoe or metal salt was added. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-21-23/rawdata/</p>09jun21a_Ctlnoxyl_030.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun21a_Ctlnoxyl_030_part.rec,  Reconstruction (Pixel Size 1.9 nm), 471.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.qqe6w7
title: Occurrence Download

description: A dataset containing 90 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Odonata",
 "Geometry POLYGON ((46.7564 -8.9557, 46.1997 -8.8713, 46.1382 -8.8989, 46.1382 -10.1057, 46.1386 -10.1063, 46.5351 -10.2533, 47.0162 -9.8227, 47.3664 -10.4507, 47.7165 -10.6099, 48.0908 -10.4735, 48.259 -10.1463, 48.1044 -9.4909, 47.7866 -9.2034, 47.3805 -9.1954, 47.0177 -9.6197, 47.0003 -9.2489, 46.7564 -8.9557))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)"
 ]
}

 The dataset includes 90 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045480-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/90qmz-wyz61
title: wild type B. subtilis

description: sacculi of sporulating wtBsubtilis
description: <strong>Tilt Series Date:</strong> 2011-07-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> subsp. subtilis str. 168</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> Leginon</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from Kit Pogliano at UCSD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation media</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/etl2011-07-05-22/3dimage_25108/</p>target20013_full.rec,  Reconstruction (Pixel Size 1.9 nm), 613.2 MB  
        
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        target20013.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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