cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/xxgp0-mpb65
title: bapta_scale7

description: Raw data files of bapta_scale7
description: <strong>Tilt Series Date:</strong> 2020-11-09</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Allium cepa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Onion peels generated like Kafle et al. 2013, incubated in HEPES >20min until freezing</p>
<strong>Sample Preparation:</strong> Glow-discharged (15mA – 1min) Quantifoil R2/2 NH2 Cu EM grids (EMSdiasum). Plunge freezing was performed with a 60/40 ratio ethane/propane mix and an FEI Vitrobot Mark IV (Thermo Fisher). Humidity was set at 50%, temperature at 20°C. Grids were first manually backblotted for 6 s in order to attach the cell wall peel firmly to the carbon, followed by two autoblottings (front and back) 5 s, maximal blot force (25) and a drain time of 3 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-7/rawdata/</p>on25-3_lam3_ts3.mrc,  Tilt Series (Pixel Size 0.33 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-7/rawdata/on25-3_lam3_ts3.mrc"
        > <i class="download icon"></i> Download </a></p>

        on25-3_lam3_ts3_rec.hdf,  Reconstruction (Pixel Size 1.32 nm), 990.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-7/3dimage_141694/on25-3_lam3_ts3_rec.hdf"
        > <i class="download icon"></i> Download </a></p>

        on25-3_lam3_ts3.rawtlt,  240.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-7/file_29902/on25-3_lam3_ts3.rawtlt"
        > <i class="download icon"></i> Download </a></p>

        on25-3_lam3_ts3.mrc.mdoc,  17.6 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/pd327-sbm66
title: non_treated_scale8

description: Raw data files of non_treated_scale8
description: <strong>Tilt Series Date:</strong> 2019-11-13</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Allium cepa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong>  Onion peels generated like Kafle et al. 2013, incubated in HEPES >20min until freezing</p>
<strong>Sample Preparation:</strong> Glow-discharged (15mA – 1min) Quantifoil R2/2 NH2 Cu EM grids (EMSdiasum). Plunge freezing was performed with a 60/40 ratio ethane/propane mix and an FEI Vitrobot Mark IV (Thermo Fisher). Humidity was set at 50%, temperature at 20°C. Grids were first manually backblotted for 6 s in order to attach the cell wall peel firmly to the carbon, followed by two autoblottings (front and back) 5 s, maximal blot force (25) and a drain time of 3 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-11-13-8/rawdata/</p>on17-1_lam2_ts2.st,  Tilt Series (Pixel Size 0.33 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-11-13-8/rawdata/on17-1_lam2_ts2.st"
        > <i class="download icon"></i> Download </a></p>

        on17-1_lam2_ts2.rec,  Tilt Series (Pixel Size 1.32 nm), 790.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-11-13-8/rawdata/on17-1_lam2_ts2.rec"
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        on17-1_lam2_ts2.rawtlt,  272.0 B  
        
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        on17-1_lam2_ts2.mrc.mdoc,  19.3 kB  
        
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DOI: 10.22002/ge061-hmg90
title: HeLa cells expressing TRIM5α-YFP

description: HeLa cell line 25 expressing stable TRIM5α-YFP. Correlated lightelectron microscopy (11062015Tom). Concentration of 500 nmblue beads (phosphorex) 4/150. 20 nm gold highly concentrated.Manual blotting with Whatman 40.HeLa cell line 25 expressingstable TRIM5α-YFP.
description: <strong>Tilt Series Date:</strong> 2015-10-29</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> HeLa cells expressing TRIM5α-YFP infected Vpr-Tomato HIV-1</p>
<strong>Strain:</strong> </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: 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> Cell line 25 and VSV-G pseudotyped virus Vpr-Tomato provided by Tom Hope</p>
<strong>Purification / Growth Conditions / Treatment:</strong> HeLa cells infected with pseudovirus Vpr-Tomato (in box). 500 µl of media and 500 µl of virus. Incubated with MG-132 (Campbell et al 2008) 6hrs. Cells were washed with warm media and incubated at 37°C before freezing.</p>
<strong>Sample Preparation:</strong> HeLa cells expressing TRIM5α-YFP infected Vpr-Tomato HIV-1</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2015-10-29-1/3dimage_71010/</p>tomography1.rec,  Reconstruction (Pixel Size 24.0 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2015-10-29-1/3dimage_71010/tomography1.rec"
        > <i class="download icon"></i> Download </a></p>

        tomography1.mrc,  Tilt Series (Pixel Size 6.0 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2015-10-29-1/rawdata/tomography1.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography1_full.rec,  Reconstruction (Pixel Size 0.0 nm), 533.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2015-10-29-1/3dimage_76100/tomography1_full.rec"
        > <i class="download icon"></i> Download </a></p>

        tomography1_full.rec,  Reconstruction (Pixel Size 0.0 nm), 533.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2015-10-29-1/3dimage_76110/tomography1_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/kn1d5-7r973
title: Myxococcus xanthus delta-pilB&T

description: Grid box YWC128Strain SA4300
description: <strong>Tilt Series Date:</strong> 2015-04-22</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</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: 180.0 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> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 2 days in 220 rpm shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-5/rawdata/</p>20150422_YWC128_20006.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-5/rawdata/20150422_YWC128_20006.mrc"
        > <i class="download icon"></i> Download </a></p>

        20150422_YWC128_20006_part121_29.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-5/3dimage_54629/20150422_YWC128_20006_part121_29.rec"
        > <i class="download icon"></i> Download </a></p>

        20150422_YWC128_20006_part121_29.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150422_YWC128_20006_part121_29.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-5/3dimage_54717/20150422_YWC128_20006_part121_29.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/j6jv8-h2h65
title: Myxococcus xanthus delta-pilB&T

description: Grid box YWC128Strain SA4300
description: <strong>Tilt Series Date:</strong> 2015-04-22</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</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: 180.0 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> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 2 days in 220 rpm shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-6/rawdata/</p>20150422_YWC128_20007.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-6/rawdata/20150422_YWC128_20007.mrc"
        > <i class="download icon"></i> Download </a></p>

        20150422_YWC128_20007_part121_49.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-6/3dimage_54631/20150422_YWC128_20007_part121_49.rec"
        > <i class="download icon"></i> Download </a></p>

        20150422_YWC128_20007_part121_40.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150422_YWC128_20007_part121_43.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-22-6/3dimage_54718/20150422_YWC128_20007_part121_43.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/jgb1j-83290
title: non_treated_scale8

description: Raw data files of non_treated_scale8
description: <strong>Tilt Series Date:</strong> 2020-02-12</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Allium cepa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Onion peels generated like Kafle et al. 2013, incubated in HEPES >20min until freezing</p>
<strong>Sample Preparation:</strong> Glow-discharged (15mA – 1min) Quantifoil R2/2 NH2 Cu EM grids (EMSdiasum). Plunge freezing was performed with a 60/40 ratio ethane/propane mix and an FEI Vitrobot Mark IV (Thermo Fisher). Humidity was set at 50%, temperature at 20°C. Grids were first manually backblotted for 6 s in order to attach the cell wall peel firmly to the carbon, followed by two autoblottings (front and back) 5 s, maximal blot force (25) and a drain time of 3 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-02-12-14/rawdata/</p>on17-1_lam3_ts1.st,  Tilt Series (Pixel Size 0.32 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-02-12-14/rawdata/on17-1_lam3_ts1.st"
        > <i class="download icon"></i> Download </a></p>

        on17-1_lam3_ts1.rec,  Reconstruction (Pixel Size 1.32 nm), 625.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-02-12-14/3dimage_141676/on17-1_lam3_ts1.rec"
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        on17-1_lam3_ts1.rawtlt,  248.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-02-12-14/file_29885/on17-1_lam3_ts1.rawtlt"
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        on17-1_lam3_ts1.mrc.mdoc,  17.5 kB  
        
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DOI: 10.22002/nav8y-atj82
title: pl_scale5

description: Raw data files of pl_scale5
description: <strong>Tilt Series Date:</strong> 2020-11-09</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Allium cepa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Onion peels generated like Kafle et al. 2013, incubated in HEPES >20min until freezing</p>
<strong>Sample Preparation:</strong> Glow-discharged (15mA – 1min) Quantifoil R2/2 NH2 Cu EM grids (EMSdiasum). Plunge freezing was performed with a 60/40 ratio ethane/propane mix and an FEI Vitrobot Mark IV (Thermo Fisher). Humidity was set at 50%, temperature at 20°C. Grids were first manually backblotted for 6 s in order to attach the cell wall peel firmly to the carbon, followed by two autoblottings (front and back) 5 s, maximal blot force (25) and a drain time of 3 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-12/rawdata/</p>on28-4_lam3_ts3.mrc,  Tilt Series (Pixel Size 0.33 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-12/rawdata/on28-4_lam3_ts3.mrc"
        > <i class="download icon"></i> Download </a></p>

        on28-4_lam3_ts3_rec.hdf,  Reconstruction (Pixel Size 1.32 nm), 707.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        on28-4_lam3_ts3.rawtlt,  272.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-11-09-12/file_29912/on28-4_lam3_ts3.rawtlt"
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        on28-4_lam3_ts3.mrc.mdoc,  19.9 kB  
        
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DOI: 10.15468/dl.hz6dnt
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Oreochromis amphimelas)",
 "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 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044003-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/xgzb2-zcj32
title: non_treated_scale6

description: Raw data files of non_treated_scale6
description: <strong>Tilt Series Date:</strong> 2019-11-13</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Allium cepa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong>  Onion peels generated like Kafle et al. 2013, incubated in HEPES >20min until freezing</p>
<strong>Sample Preparation:</strong> Glow-discharged (15mA – 1min) Quantifoil R2/2 NH2 Cu EM grids (EMSdiasum). Plunge freezing was performed with a 60/40 ratio ethane/propane mix and an FEI Vitrobot Mark IV (Thermo Fisher). Humidity was set at 50%, temperature at 20°C. Grids were first manually backblotted for 6 s in order to attach the cell wall peel firmly to the carbon, followed by two autoblottings (front and back) 5 s, maximal blot force (25) and a drain time of 3 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-11-13-1/rawdata/</p>on14-3_lam1_ts1.st,  Tilt Series (Pixel Size 0.33 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-11-13-1/rawdata/on14-3_lam1_ts1.st"
        > <i class="download icon"></i> Download </a></p>

        on14-3_lam1_ts1.hdf,  Reconstruction (Pixel Size 1.32 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2019-11-13-1/3dimage_141653/on14-3_lam1_ts1.hdf"
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        on14-3_lam1_ts1.rawtlt,  264.0 B  
        
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        on14-3_lam1_ts1.mrc.mdoc,  18.7 kB  
        
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