cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/zy9t3-xmk51
title: Alongum

description: Alongum_periplasmiclayers
description: <strong>Tilt Series Date:</strong> 2012-05-20</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: (-30.0°, 30.0°), 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> WesleyChen helped remove layers</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/etl2012-05-20-11/rawdata/</p>AlongLys0013.mrc,  Tilt Series (Pixel Size 0.95 nm), 677.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-11/rawdata/AlongLys0013.mrc"
        > <i class="download icon"></i> Download </a></p>

        13_full.rec,  Reconstruction (Pixel Size 1.95 nm), 825.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-11/3dimage_56738/13_full.rec"
        > <i class="download icon"></i> Download </a></p>

        AlongLys0013_full.rec,  Reconstruction (Pixel Size 1.95 nm), 309.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-11/3dimage_56739/AlongLys0013_full.rec"
        > <i class="download icon"></i> Download </a></p>

        bot.rec,  Reconstruction (Pixel Size 1.95 nm), 16.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-11/3dimage_56740/bot.rec"
        > <i class="download icon"></i> Download </a></p>

        mid.rec,  Reconstruction (Pixel Size 1.95 nm), 16.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-11/3dimage_56741/mid.rec"
        > <i class="download icon"></i> Download </a></p>

        top.rec,  Reconstruction (Pixel Size 1.95 nm), 16.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-11/3dimage_56742/top.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gw123-1mh24
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/etl2014-02-01-12/rawdata/</p>c1_60001.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/etl2014-02-01-12/rawdata/c1_60001.mrc"
        > <i class="download icon"></i> Download </a></p>

        c1_60001_part121_4.rec,  Reconstruction (Pixel Size 0.0 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-12/3dimage_49217/c1_60001_part121_4.rec"
        > <i class="download icon"></i> Download </a></p>

        slicer000.tif,  2.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-12/file_10945/slicer000.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer001.tif,  2.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-12/file_10946/slicer001.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer002.tif,  2.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-12/file_10947/slicer002.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer003.tif,  2.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-12/file_10948/slicer003.tif"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/mbr9n-2gn26
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>
  etl2014-02-01-4_slicer6986.jpg: pilli etl2014-02-01-4_slicer6988.jpg: Peptidoglycan etl2014-02-01-4_slicer6990.jpg: filament etl2014-02-01-4_slicer6991.jpg: filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-4/rawdata/</p>c10004.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/etl2014-02-01-4/rawdata/c10004.mrc"
        > <i class="download icon"></i> Download </a></p>

        c10004_full.rec,  Reconstruction (Pixel Size 0.0 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-4/3dimage_49231/c10004_full.rec"
        > <i class="download icon"></i> Download </a></p>

        slicer000.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-4/file_10994/slicer000.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer001.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-4/file_10995/slicer001.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer002.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-4/file_10996/slicer002.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer003.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-02-01-4/file_10997/slicer003.tif"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6nv8v-pdw35
title: Agrobacterium tumefaciens C58

description: Wild type
description: <strong>Tilt Series Date:</strong> 2014-01-28</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> Cells grown on plates, scraped off and grown o/n in a drop</p>
<strong>Sample Preparation:</strong> Vitrobot, manual blot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-01-28-16/rawdata/</p>c58_drop0009.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/etl2014-01-28-16/rawdata/c58_drop0009.mrc"
        > <i class="download icon"></i> Download </a></p>

        c58_drop0009_full.rec,  Reconstruction (Pixel Size 0.0 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-01-28-16/3dimage_49317/c58_drop0009_full.rec"
        > <i class="download icon"></i> Download </a></p>

        slicer000.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-01-28-16/file_11318/slicer000.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer001.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-01-28-16/file_11319/slicer001.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer002.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-01-28-16/file_11320/slicer002.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer003.tif,  2.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-01-28-16/file_11321/slicer003.tif"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8444m-hrp45
title: Agro C1 induction 28C

description: Agro C1, no Ti plasmid, induced at 28 for 24h in liquid AB+AS
description: <strong>Tilt Series Date:</strong> 2014-03-25</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> Agro C1, no Ti plasmid, induced at 28 in liquid AB+AS</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
  etl2014-03-25-11_slicer9866.jpg: Agrobacterium tumefaciens .  comb
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-03-25-11/rawdata/</p>Agro_C1_Pat0011.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/etl2014-03-25-11/rawdata/Agro_C1_Pat0011.mrc"
        > <i class="download icon"></i> Download </a></p>

        Agro_C1_Pat0011.rec,  Reconstruction (Pixel Size 0.0 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-03-25-11/3dimage_49428/Agro_C1_Pat0011.rec"
        > <i class="download icon"></i> Download </a></p>

        slicer007.tif,  3.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-03-25-11/file_11634/slicer007.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer008.tif,  3.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-03-25-11/file_11635/slicer008.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer009.tif,  3.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-03-25-11/file_11636/slicer009.tif"
        > <i class="download icon"></i> Download </a></p>

        slicer010.tif,  3.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2014-03-25-11/file_11637/slicer010.tif"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16275154
title: Genetic diversity and population structure of black pine (Pinus nigra Arn.) in Mt. Athos, northern Greece

description: This dataset contains genotype data from 67 individuals from four black pine (Pinus nigra) populations (Mt. Athos, Sithonia, Thassos, and Perama) in north Greece. Genotyping was conducted using fragment analysis across seven polymorphic loci. 

It is available in CSV format containing data for each individual and defining sampling population, location, plant identifier code, geographic coordinates (longitude, latitude, altitude) and polymorphic loci.
description: The European black pine (Pinus nigra subsp. nigra) persists in scattered montane stands across Greece, where isolated populations harbor genetic variation shaped by local environments and demographic history. In this study, we assessed the genetic diversity and population structure of P. nigra using nuclear microsatellite markers (nSSRs) across four populations: Mt. Athos, Sithonia, Thassos, and Perama. A total of 67 individuals were genotyped, and seven high-quality polymorphic loci were retained after rigorous filtering. The Mt. Athos population exhibited the highest allelic richness and heterozygosity, with all loci polymorphic and a low inbreeding coefficient after null allele correction. In contrast, the Perama population displayed reduced diversity, fewer polymorphic loci, and persistent heterozygote deficits. Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC) revealed weak overall population structure, with Perama genetically distinct from the other sites. Spatial Principal Component Analysis (sPCA) further uncovered an east–west cline within Athos and localized structure potentially shaped by both natural isolation and human influence. These findings highlight regional variation in genetic diversity within P. nigra and identify Athos as a genetically rich population of particular interest. The results provide a foundation for long-term monitoring and support informed strategies for the management and conservation of P. nigra in Greece.
description: We acknowledge that this research was partially funded by the project STrategic Environmental Management in Mount Athos under Climate Change (LIFE STEMMA ATHOS, https://lifestemma.eu).
DOI: 10.22002/jc1fh-3qx93
title: HeLa cells expressing TRIM5α-YFP

description: 4 hours incubation MG-132 (0.4 ul) 1 μg/ml.
description: <strong>Tilt Series Date:</strong> 2016-05-05</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> Hela cells expressing TRIM5a-YFP</p>
<strong>Strain:</strong> </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: -10.0 μm,  magnification: 18000x. </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> Tom Hope</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown on R2/2 London finder grids coated with fibronectin</p>
<strong>Sample Preparation:</strong> Manual Blotting</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-05-8/rawdata/</p>tomography8.mrc,  Tilt Series (Pixel Size 6.167 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-05-8/rawdata/tomography8.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography8.rec,  Reconstruction (Pixel Size 24.668 nm), 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-05-8/3dimage_118364/tomography8.rec"
        > <i class="download icon"></i> Download </a></p>

        trimsirt.rec,  Reconstruction (Pixel Size 0.0 nm), 296.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-05-8/3dimage_118475/trimsirt.rec"
        > <i class="download icon"></i> Download </a></p>

        tomography8secondreverse2_full.rec,  Reconstruction (Pixel Size 0.0 nm), 668.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-05-8/3dimage_118476/tomography8secondreverse2_full.rec"
        > <i class="download icon"></i> Download </a></p>

        sirt.rec,  Reconstruction (Pixel Size 0.0 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-05-8/3dimage_118477/sirt.rec"
        > <i class="download icon"></i> Download </a></p>

        trimsirt.rec.nad,  296.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2016-05-05-8/file_27428/trimsirt.rec.nad"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16275153
title: Genetic diversity and population structure of black pine (Pinus nigra Arn.) in Mt. Athos, northern Greece

description: This dataset contains genotype data from 67 individuals from four black pine (Pinus nigra) populations (Mt. Athos, Sithonia, Thassos, and Perama) in north Greece. Genotyping was conducted using fragment analysis across seven polymorphic loci. 

It is available in CSV format containing data for each individual and defining sampling population, location, plant identifier code, geographic coordinates (longitude, latitude, altitude) and polymorphic loci.
description: The European black pine (Pinus nigra subsp. nigra) persists in scattered montane stands across Greece, where isolated populations harbor genetic variation shaped by local environments and demographic history. In this study, we assessed the genetic diversity and population structure of P. nigra using nuclear microsatellite markers (nSSRs) across four populations: Mt. Athos, Sithonia, Thassos, and Perama. A total of 67 individuals were genotyped, and seven high-quality polymorphic loci were retained after rigorous filtering. The Mt. Athos population exhibited the highest allelic richness and heterozygosity, with all loci polymorphic and a low inbreeding coefficient after null allele correction. In contrast, the Perama population displayed reduced diversity, fewer polymorphic loci, and persistent heterozygote deficits. Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC) revealed weak overall population structure, with Perama genetically distinct from the other sites. Spatial Principal Component Analysis (sPCA) further uncovered an east–west cline within Athos and localized structure potentially shaped by both natural isolation and human influence. These findings highlight regional variation in genetic diversity within P. nigra and identify Athos as a genetically rich population of particular interest. The results provide a foundation for long-term monitoring and support informed strategies for the management and conservation of P. nigra in Greece.
description: We acknowledge that this research was partially funded by the project STrategic Environmental Management in Mount Athos under Climate Change (LIFE STEMMA ATHOS, https://lifestemma.eu).