cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/9wby2-n8m11
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 induced with xylose for 20 hours. No 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/zla2009-06-21-5/rawdata/</p>09jun21a_Ctlnomet_009.mrc,  Tilt Series (Pixel Size 0.95 nm), 679.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-21-5/rawdata/09jun21a_Ctlnomet_009.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jun21a_Ctlnomet_009_part.rec,  Reconstruction (Pixel Size 1.9 nm), 471.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/f2k5b-gdv02
title: Hyphomonas session9 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-07</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: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 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...</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/jsa2009-03-07-2/rawdata/</p>09mar07a_36c_002.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-2/rawdata/09mar07a_36c_002.mrc"
        > <i class="download icon"></i> Download </a></p>

        09mar07a_36c_002_full.rec,  Reconstruction (Pixel Size 1.264 nm), 419.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ywd2zn
title: Occurrence Download

description: A dataset containing 21198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hydrilla verticillata"
 ]
}

 The dataset includes 21198 records from 358 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007109-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/rbffm-he774
title: Hyphomonas session9 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-07</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: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 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...</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/jsa2009-03-07-41/rawdata/</p>09mar07a_36c_042.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09mar07a_36c_042_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/jsa2009-03-07-41/3dimage_6949/09mar07a_36c_042_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/w11em-b2850
title: E.coli "strain8" Tsr-A413G

description: CheA-on state
description: <strong>Tilt Series Date:</strong> 2011-11-28</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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 from Sandy Parkinson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in TB medium</p>
<strong>Sample Preparation:</strong> Lysed with Penicillin for one hour</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2011-11-28-10/rawdata/</p>strain8nov2011_0010.mrc,  Tilt Series (Pixel Size 0.644 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2011-11-28-10/rawdata/strain8nov2011_0010.mrc"
        > <i class="download icon"></i> Download </a></p>

        strain8nov2011_0010_part.rec,  Reconstruction (Pixel Size 1.288 nm), 516.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2011-11-28-10/3dimage_15829/strain8nov2011_0010_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/jn6yg-tjz21
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/etl2011-03-29-28/3dimage_25450/</p>11mar29a_gr4_034_full.rec,  Reconstruction (Pixel Size 1.9 nm), 943.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        11mar29a_gr4_034.mrc,  Tilt Series (Pixel Size 0.95 nm), 922.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-03-29-28/rawdata/11mar29a_gr4_034.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/p94vd-r0z72
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>
  jsa2009-07-14-3_slicer8707.jpg: DNA .  Hyphomonas neptunium
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-3/rawdata/</p>09jul14a_b200c_003.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-3/rawdata/09jul14a_b200c_003.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jul14a_b200c_003_full.rec,  Reconstruction (Pixel Size 1.264 nm), 367.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-3/3dimage_8184/09jul14a_b200c_003_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/58y48-93690
title: (D161A)MamK-GFP/wild type

description: Raw data files of (D161A)MamK-GFP/wild type
description: <strong>Tilt Series Date:</strong> 2009-11-23</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Magnetospirillum magneticum</p>
<strong>Strain:</strong> AMB-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: -16.0 μm,  magnification: 18000x. </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> Cells provided by Arash Komeili; data collected by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> (Probably) stationary phase </p>
<strong>Sample Preparation:</strong> Quantifoil R2/2, R2/1, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-11-23-34/rawdata/</p>09nov23a_D161Awt_034.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09nov23a_D161Awt_034_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-11-23-34/3dimage_9693/09nov23a_D161Awt_034_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6073/pasta/40c17da3a4fe28884f62a4a8bbd46f16
title: O. mykiss passages at the Stanislaus River weir, 2005-2025

description: The Central Valley Project Improvement Act (CVPIA) provides funds to aid the San Joaquin Basin Steelhead Collaborative and initiate a Steelhead Life-Cycle Monitoring Program. This dataset includes observations of O. mykiss in the Stanislaus River during the steelhead spawning migration period, September through May. Fish are observed at an Alaskan-style weir outfitted with a VAKI Riverwatcher fish counting device. The counting device provides visual records of upstream passing individuals that are later reviewed by an experienced biologist. During times when the counting device is offline, a continuous video feed is reviewed to provide counts and identifications of passing fish. The length of passing fish is estimated using a known body depth to length ratio derived from individuals trapped and measured at the weir. The weir also has a trap box that, when closed, allows investigators to physically capture fish for measurements, biological sample collection, and injection of a PIT tag. There is also a PIT tag antenna affixed to the weir allowing detection of PIT tagged fish. There are three datasets currently associated with this project, 1) passage data for all O. mykiss from 2005 through 2025, 2) O. mykiss that were captured and processed from the trap, and 3) PIT tag detections from the PIT antenna.
DOI: 10.22002/me29p-ata47
title: M222R chemoreceptor mutant

description: M222R HAMP mutant locked in 'CHeA inactivating state'
description: <strong>Tilt Series Date:</strong> 2010-03-19</p>
<strong>Data Taken By:</strong> Ariane Briegel</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: -10.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> John Parkinson </p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in TB medium, induced with salycilate (0.6 µM) for three hours, then penicillin treated for one hour </p>
  aba2010-03-19-18_slicer9750.jpg: Escherichia coli .  nested vesicle aba2010-03-19-18_slicer9751.jpg: Escherichia coli .  vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-03-19-18/rawdata/</p>10mar19a_EcoliM222K_018.st,  Tilt Series (Pixel Size 0.632 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10mar19a_EcoliM222K_018.rec,  Reconstruction (Pixel Size 0.632 nm), 309.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/k2wvf-nv166
title: HeLa CHMP4A+VPS4DN

description: HeLa cells transfected with CHMP4A & VPS4DN constructs
description: <strong>Tilt Series Date:</strong> 2011-02-09</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HeLa cells</p>
<strong>Strain:</strong> ATCC</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: -6.0 μm,  magnification: 22500x. </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> Constructs provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with polyfect</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-02-09-3/rawdata/</p>11feb09b_C50-4d_003.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11feb09b_C50-4d_003_full.rec,  Reconstruction (Pixel Size 2.0 nm), 411.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9cvrz-r1s44
title: Agro Bald VirB8-GFP

description: the bald strain lacks flagellin 1-3 and is considered non-motile
description: <strong>Tilt Series Date:</strong> 2013-07-02</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: -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> Pat Zambryski</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells were grown at 19C and induced for T4SS</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-07-02-6/rawdata/</p>bald_gfp20007.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2013-07-02-6/rawdata/bald_gfp20007.mrc"
        > <i class="download icon"></i> Download </a></p>

        bald_gfp20007_part121_3.rec,  Reconstruction (Pixel Size 1.92 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/a2r57-h1625
title: Eco 031910 MP49

description: Escherichia coli, 10mar24a_MP_49III_050,
description: <strong>Tilt Series Date:</strong> 2010-03-24</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/mpa2010-03-24-32/rawdata/</p>10mar24a_MP_49III_050.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10mar24a_MP_49III_050_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.86r346
title: Occurrence Download

description: A dataset listing the 53 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-15.81829 28.00284,-15.81903 28.00104,-15.81597 28.00037,-15.81503 28.00164,-15.81511 28.00208,-15.81691 28.00265,-15.81829 28.00284))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 53 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007080-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/gah2a-4qa72
title: MT310_xyl+_aurothioglucose(50um)

description: Raw data files of MT310_xyl+_aurothioglucose(50um)
description: <strong>Tilt Series Date:</strong> 2009-10-21</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: (-63.0°, 63.0°), 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; cells were cultured and treated by Zhuo Li; data were collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were induced by xylose for ? hours and treated by aurothioglucose for ? hours</p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-21-20/rawdata/</p>09oct21a_MT310Auglu50_020.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        09oct21a_MT310Auglu50_020_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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