cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/pe5a4-2mx83
title: B. subtilis 3267

description: Raw data files of B. subtilis 3267
description: <strong>Tilt Series Date:</strong> 2011-12-08</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> AD3267, ponA null, Alp7A-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>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> Joe Pogliano</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells were grown in LB</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-08-1/rawdata/</p>3267a0001.mrc,  Tilt Series (Pixel Size 1.9 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-08-1/rawdata/3267a0001.mrc"
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        3267a0001_full.rec,  Reconstruction (Pixel Size 3.8 nm), 825.8 MB  
        
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DOI: 10.22002/g0d1c-j9s98
title: E. coli (pLE7, 20 uM IPTG)

description: Cells contain WT MreB in the chromosome plus an N-terminal YFP fusion to MreB (YFP-MreB) on the plasmid pLe7. pLE7 also confers a resistance to ampicillin.
description: <strong>Tilt Series Date:</strong> 2011-06-02</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Escherichia coli</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: None μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> Gift from Larry Rothfield</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown at 37 degrees celsius to OD600=0.2 then 20 uM IPTG was added for 2 hours of growth before freezing.</p>
<strong>Sample Preparation:</strong> Vitrobot plunge freezing</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2011-06-02-21/rawdata/</p>20110602_PLE7_26.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        20110602_PLE7_26_full.rec,  Reconstruction (Pixel Size 1.9 nm), 825.8 MB  
        
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DOI: 10.22002/ph77x-by423
title: Agro C58

description: Wild type Agrobacterium C58
description: <strong>Tilt Series Date:</strong> 2013-09-13</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: 34x. </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> Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown on agar plates for 2 days on Au grids</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-09-13-53/rawdata/</p>C58_au_34k0054.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
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        C58_au_34k0054_part121_12.rec,  Reconstruction (Pixel Size 1.28 nm), 801.8 MB  
        
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DOI: 10.22002/bwv7h-w3r52
title: CLEM of TRIM5a-YFP in HeLa cells

description: Correlated light electron microscopy. Concentration of red 200 nm beads 1/300. 10 nm gold. Manual blotting. Cells grown on grids for 2 days and look vesiculated
description: <strong>Tilt Series Date:</strong> 2014-07-10</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: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -8.4 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> Tom Hope and Wes Sundquist</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Gold London finder grids glow discharged twice. Concentration of red 200 nm beads 1/300 on grid. 10 nm gold. Manual blotting. Cells grown on grids for 2 days and look vesiculated.</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-07-10-5/rawdata/</p>tomographyh13nosignalhole.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
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        tomographyh13nosignalhole_full.rec,  Reconstruction (Pixel Size 1.56 nm), 890.9 MB  
        
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DOI: 10.15468/dl.ry8tdb
title: Occurrence Download

description: A dataset containing 249746 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((73.24694 25.04176,104.06323 25.04176,104.06323 44.88618,73.24694 44.88618,73.24694 25.04176))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Liliopsida"
 ]
}

 The dataset includes 249746 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007051-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/s9em6-x7239
title: Bsubtilis_ponA_sacculi

description: Bsubtilis_sacculi_ponA
description: <strong>Tilt Series Date:</strong> 2012-02-11</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> MJ007, ponA null</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/etl2012-02-11-18/rawdata/</p>MJsacculi0024.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/etl2012-02-11-18/rawdata/MJsacculi0024.mrc"
        > <i class="download icon"></i> Download </a></p>

        MJsacculi0024_full.rec,  Reconstruction (Pixel Size 1.9 nm), 877.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-02-11-18/3dimage_26178/MJsacculi0024_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/k5mt0-84d06
title: Wild type control

description: Raw data files of Wild type control
description: <strong>Tilt Series Date:</strong> 2009-08-01</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: 200.0 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> Experiments were done by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase NA1000 cells.</p>
<strong>Sample Preparation:</strong> 10 nm gold </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-44/rawdata/</p>09aug01a_noaddctl1_044.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09aug01a_noaddctl1_044_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7f031-cx906
title: sporulating Bsubtilis MJ007

description: sporulating Bsubtilis MJ007, skinny Bacillus
description: <strong>Tilt Series Date:</strong> 2011-03-29</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> MJ007, ponA null</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/etl2011-03-29-20/3dimage_25434/</p>29_full.rec,  Reconstruction (Pixel Size 1.9 nm), 692.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-03-29-20/3dimage_25434/29_full.rec"
        > <i class="download icon"></i> Download </a></p>

        11mar29a_gr4_021.mrc,  Tilt Series (Pixel Size 0.95 nm), 947.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-03-29-20/rawdata/11mar29a_gr4_021.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16277421
title: Positive drought feedbacks increase tree mortality risk in dry woodlands of the US Southwest

description: This data archive includes data, R code, and model objects used to analyze drought-driven changes in the structure and composition of pinyon-juniper woodlands of northern Arizona, USA. The archive includes records of >5,000 individual trees, which were repeatedly measured over the period of 1998 to 2023, as well as associated ground cover and field-derived soils information. Lastly, it includes downscaled climate data and other spatial datasets associated with the field sites. For additional details, see the "README.html" file in this archive. An abstract for this project is as follows:

Global changes in temperature and aridity are increasing the frequency of extreme drought events. Such changes can have pronounced impacts on dryland ecosystems which exist at the margins of plant physiological tolerances. Pinyon-juniper (PJ) woodlands – a dryland vegetation type spanning 40 million ha in western North America – is a model system for the impacts of drought, where recurrent short-interval drought events may trigger feedback mechanisms that influence future drought resistance. Leveraging a long-term monitoring network in PJ woodlands of the United States (US) Southwest, we sought to understand how interactions between recurrent drought events influence tree mortality risk. We developed generalized linear mixed models to predict patterns of recent (i.e., 2014-2023) tree mortality based on biophysical variables, tree size, and prior drought-driven changes (ca. 1998-2014) in forest conditions. We then used these models to quantify how mortality risk has shifted over time. Tree density and stand basal area declined substantially throughout our 1998 to 2023 monitoring period. Since 2014, tree mortality was more common and spatially extensive than new tree recruitment, and nearly half of the surviving trees experienced crown dieback. Tree size influenced biotic interactions and responses to environmental conditions, and soil organic matter and mycorrhizal fungi communities buffered individuals against drought. Shifts in woodland demographics (e.g., reduced stand densities, crown dieback) led to a 30% relative increase in mortality risk between 2014 and 2023 for trees that survived this period. Recent drought events have triggered widespread tree mortality and dieback in PJ woodlands of the US Southwest. These events are also increasing future tree mortality risk, overcoming system inertia created by local edaphic conditions and compensatory responses.
DOI: 10.22002/1hvsc-gd497
title: GFP-MreB fusion methanol control

description: Raw data files of GFP-MreB fusion methanol control
description: <strong>Tilt Series Date:</strong> 2009-08-01</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: 200.0 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, REACH</p>
<strong>Collaborators and Roles:</strong> Experiments were done by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The GFP-MreB-expressing NA1000 cells were cultured to exponential phase and treated with methanol as a control.</p>
<strong>Sample Preparation:</strong> 10 nm gold.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-107/rawdata/</p>09aug01a_methanolgfmr1_107.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        09aug01a_methanolgfmr1_107_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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DOI: 10.22002/25xt5-jgg92
title: HUVECs infx pNLGFP

description: single tilt. constant angular increment, step: 1.0. tilt range: (-60, 60).         dosage: 150/A2. defocus: -6um. magnification: 19000.
description: <strong>Tilt Series Date:</strong> 2013-07-05</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HUVECs</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: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> pNLGFP obtained from Irvin Chen (UCLA)</p>
<strong>Sample Preparation:</strong> Whole cells were grown on Au finder grids and infected with pNLGFP-VSVG. Sample frozen 24h post infection</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-07-05-5/rawdata/</p>13jul05_C161-2_HUVECspnl24hPI_montage_33x33_0024.mrc,  Tilt Series (Pixel Size 0.56 nm), 3.3 GB  
        
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        13jul05_C161-2_HUVECspnl24hPI_montage_33x33_0024_full.rec,  Reconstruction (Pixel Size 2.24 nm), 602.8 MB  
        
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DOI: 10.22002/yv1a9-18e83
title: AimB depletion w/ Glucose

description: Raw data files of AimB depletion w/ Glucose
description: <strong>Tilt Series Date:</strong> 2009-07-30</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> The AimB depletion strain was constructed by John Werner in Zemer Gitai's lab. Depletion was done by Zhuo Li. Data were collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The AimB depletion strain was depleted serially with 0.2% glucose. </p>
<strong>Sample Preparation:</strong> 10 nm</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-11/rawdata/</p>09jul30a_AimBglu_011.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        09jul30a_AimBglu_011_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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DOI: 10.22002/xv4cr-dhd74
title: HUVECs-pNLGFP-VPS4DN

description: HUVECs cells were first transfected with VPS4DN construct using Nucleofector Kit. 4.5 h post-transfection cells were infected with pNLGFP-VSVG by spinoculation and then frozen 24 h post infection.  Sample# C68
description: <strong>Tilt Series Date:</strong> 2011-04-14</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HUVECs</p>
<strong>Strain:</strong> </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: 22500x. </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> VPS4DN construct provided by Wes Sundquist. pNL4GFP provirus construct from Irvin Chen (UCLA). Cells transfected, infected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids, transfected and then infected</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-04-14-20/rawdata/</p>11apr14b_C68-2b_041.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        11apr14b_C68-2b_041_full.rec,  Reconstruction (Pixel Size 2.0 nm), 3.1 GB  
        
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