cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/f4m55-wq543
title: wt_serum_blotfrombehind

description: This is a sample of wt grown in serum bottle that made nanowires.
description: <strong>Tilt Series Date:</strong> 2015-07-26</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2.0°, constant angular increment, dosage: 150.0 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> Moh and Sahand</p>
<strong>Sample Preparation:</strong> The sample was put on the C side (glow discharged side) on the left. The blotting was done from behind on the rt side. Vitrobot was used. All other vitrobot conditions are the same.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-07-26-46/rawdata/</p>10047.mrc,  Tilt Series (Pixel Size 0.48 nm), 1.7 GB  
        
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        10047_part61_3.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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DOI: 10.22002/mnc4h-rvj47
title: WT LP01 from Liu lab, Yale

description: Type four secretion system, T4SS
description: <strong>Tilt Series Date:</strong> 2016-11-28</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -5.0 μm,  magnification: 15500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Data collected by Bo Hu in Jun Liu lab at Yale from their Polara. Partial WT strain data set. Primary literature:  doi: 10.1038/s41564-018-0165-z</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-322/rawdata/</p>T4SSWTNov26A029_driftcorr.mrc,  Tilt Series (Pixel Size 0.25 nm), 2.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        T4SSWTNov26A029_driftcorr.rec,  Reconstruction (Pixel Size 1.0 nm), 2.3 GB  
        
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DOI: 10.22002/z6wrp-xtr05
title: WT LP01 from Liu lab, Yale

description: Type four secretion system, T4SS
description: <strong>Tilt Series Date:</strong> 2016-11-28</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-51.0°, 51.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -5.0 μm,  magnification: 15500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Data collected by Bo Hu in Jun Liu lab at Yale from their Polara. Partial WT strain data set. Primary literature:  doi: 10.1038/s41564-018-0165-z</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2016-11-28-288/rawdata/</p>T4SSWTNov25A033_driftcorr.mrc,  Tilt Series (Pixel Size 0.25 nm), 1.8 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        T4SSWTNov25A033_driftcorr.rec,  Reconstruction (Pixel Size 1.0 nm), 2.3 GB  
        
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DOI: 10.22002/3btfk-znx73
title: Vibrio cholerae C6706 ∆lacZ

description: Wild Type Vibrio
description: <strong>Tilt Series Date:</strong> 2015-06-02</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O1 biovar El Tor</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -8.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Janelia Titan</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> Simon Ringgaard</p>
  aba2015-06-02-1_slicer13862.jpg:  .  [2015-11-21 00:33:12] hollow spheres at bottom resemble structures seen in ab2015-06-02-29 yc2015-06-17-31 et2015-05-15-5-andrew
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-06-02-1/rawdata/</p>VibrioLacZ0001.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-06-02-1/rawdata/VibrioLacZ0001.mrc"
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        VibrioLacZ0001_part121_12.rec,  Reconstruction (Pixel Size 1.28 nm), 688.9 MB  
        
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DOI: 10.22002/65by0-7g052
title: immunogoldMtrc_wt

description: This is wt made in perfusion chamber and fixed with 2.5% glutaraldehyde and immune-gold labeled for Mtr complex. The grid # is PS123-#3
description: <strong>Tilt Series Date:</strong> 2015-12-29</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 143.0 eV/Å²,  defocus: -6.0 μm,  magnification: 34000x. </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> Sahand and Moh, USC</p>
<strong>Sample Preparation:</strong> The sample was pulled out of Dh2O, was loaded on vitrobot with C side on left. Before blotting added 4ul of water. Blotting conditions: blot force -6, blot time -3.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-12-29-10/3dimage_71963/</p>atlas2_sq150010_full.rec,  Reconstruction (Pixel Size 1.28 nm), 445.4 MB  
        
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        atlas2_sq150010.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
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DOI: 10.15468/dl.b283gw
title: Occurrence Download

description: A dataset containing 181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pinus ponderosa",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 181 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047337-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/av7kk-dfm16
title: Vibrio cholerae

description: Raw data files of Vibrio cholerae
description: <strong>Tilt Series Date:</strong> 2015-10-01</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> PM22, lacZ- Δvc1397 Δvc1402</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -8.0 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> Simon Ringgaard</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Briegel, A., Ortega, D. R., Mann, P., Kjaer, A., Ringgaard, S. and Jensen, G. J. (2016). Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM. Proc Natl Acad Sci U S A 113, 10412-10417.</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-10-01-42/3dimage_69814/</p>PM22deltaCheA1trippleWsetB0005_part121_3.rec,  Reconstruction (Pixel Size 1.28 nm), 712.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        PM22deltaCheA1trippleWsetB0005.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.jj56ue
title: Occurrence Download

description: A dataset containing 587 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Arbutus arizonica"
 ]
}

 The dataset includes 587 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047338-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/gr1kb-ydd24
title: TopJ + MPN119

description: Raw data files of TopJ + MPN119
description: <strong>Tilt Series Date:</strong> 2016-06-06</p>
<strong>Data Taken By:</strong> Songye Chen</p>
<strong>Species / Specimen:</strong> Mycoplasma pneumoniae</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 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> Edward Sheppard from Duncan Krause's lab prepared the cell culture</p>
  scy2016-06-06-10_slicer16953.jpg: attachment organelles scy2016-06-06-10_slicer16954.jpg: attachment organelle scy2016-06-06-10_slicer16955.jpg: attachment organelle scy2016-06-06-10_slicer16956.jpg: attachment organelle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scy2016-06-06-10/rawdata/</p>at90010.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        at90010_part131_30.rec,  Reconstruction (Pixel Size 1.56 nm), 356.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.2w44pj
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Phasianus versicolor",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047340-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/7wcy2-41t61
title: Mycobacterium marinum

description: Grown on 2x LB to induce sporulation
description: <strong>Tilt Series Date:</strong> 2015-10-13</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Mycobacterium marinum</p>
<strong>Strain:</strong> </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: -8.0 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> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> Will DePas from Dianne Newman's lab grew the cells</p>
<strong>Sample Preparation:</strong> Cells were frozen with Vitrobot Mark 4. Grids were positively glow discharged.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2015-10-13-11/3dimage_70189/</p>Mmarinum2_oct20150001.rec,  Reconstruction (Pixel Size 1.92 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Mmarinum2_oct20150001.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7s7k3-0b152
title: TopJ + MPN119

description: Raw data files of TopJ + MPN119
description: <strong>Tilt Series Date:</strong> 2016-06-06</p>
<strong>Data Taken By:</strong> Songye Chen</p>
<strong>Species / Specimen:</strong> Mycoplasma pneumoniae</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 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> Edward Sheppard from Duncan Krause's lab prepared the cell culture</p>
  scy2016-06-06-30_slicer16994.jpg: attachment organelles scy2016-06-06-30_slicer16995.jpg: attachment organelle scy2016-06-06-30_slicer16996.jpg: attachment organelle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scy2016-06-06-30/rawdata/</p>at90030.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
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        at90030_full.rec,  Reconstruction (Pixel Size 1.56 nm), 356.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/0v4s2-fwn74
title: nanochemowt

description: This is my fourth attempt to grow Shewanella. This culture is wt grown at caltech in chemostat.Frozen here in vitrobot.
description: <strong>Tilt Series Date:</strong> 2015-06-02</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</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: -7.0 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> Moh and Sahand USC</p>
<strong>Sample Preparation:</strong> This sample was frozen after being in oxygen deficiency for 16h. Checked by SEM and had nanowires. Vitrobot freezing conditions 6s blot force, 3s blot time, 1s drain time, 4ul on grid.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-06-02-30/rawdata/</p>nanochemo_atlas10038.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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        nanochemo_atlas10038_full.rec,  Reconstruction (Pixel Size 1.92 nm), 534.5 MB  
        
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DOI: 10.22002/bs3tv-hb810
title: Vibrio DeltaVC1403

description: Vibrio cholerae strain CO35 (delta VC1403)cytoplasmic chemoreceptor in chemotaxis operon with CheA1(F9 chemotaxis system)
description: <strong>Tilt Series Date:</strong> 2015-01-16</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O1 biovar El Tor</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -8.0 μm,  magnification: 34000x. </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 generated by Catherine Oikonomou</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown 24 hrs in LB at 30C, diluted 150 µl into 2 ml Ca-HEPES buffer, grown 16 hours at 30C</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-01-16-3/rawdata/</p>VibrioCO35tomo0003.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        VibrioCO35tomo0003_full.rec,  Reconstruction (Pixel Size 1.28 nm), 712.7 MB  
        
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DOI: 10.22002/nnj2w-dqt75
title: Protein complex

description: BG505 SOSIP trimer-354BG18 Fab-179nc75 Fab complex
description: <strong>Tilt Series Date:</strong> 2015-11-23</p>
<strong>Data Taken By:</strong> Songye Chen</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 41000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> motioncorr_v2.1, IMOD patch tracking</p>
<strong>Collaborators and Roles:</strong> Haoqing Wang @ Pamela Bjorkman lab prepared the sample</p>
<strong>Sample Preparation:</strong> 160mg/ml frozen on C-flat 400 Mesh Cu grid</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scy2015-11-23-15/3dimage_71148/</p>atlas1_0035_mcorr.rec,  Reconstruction (Pixel Size 1.04 nm), 356.4 MB  
        
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        atlas1_0035_mcorr.mrc,  Tilt Series (Pixel Size 0.26 nm), 3.4 GB  
        
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DOI: 10.22002/ec7am-j1c79
title: nanowire+type4pili+Chemo

description: Raw data files of nanowire+type4pili+Chemo
description: <strong>Tilt Series Date:</strong> 2015-05-11</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: -7.0 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> Moh and Sahand</p>
<strong>Sample Preparation:</strong> This sample is from the chemostat. Nothing has been mutated. So its a wt chemostat sample</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-05-11-14/rawdata/</p>051115_nano0014.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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        051115_nano0014_part121_7.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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