cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/raa3t-dqg52
title: V. cholerae RT4236 (refreshed)

description: Classical strain with ctxA deletion.Cell harbors pMT5 plasmid (inducible toxT).
description: <strong>Tilt Series Date:</strong> 2015-12-19</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 160.0 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 from Ronald K. Taylor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> V. cholerae 0395-N1 pMT5 grown in 5ml LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin in glass tube shaking for overnight. After took the tube out from shaker, place the tube on bench for ~20 min, supernatant was removed and pellet was resuspended by gentle pipetting in 1ml fresh LB without IPTG nor ampicillin. Culture was incubated at room temperature for ~20 min before mixing with gold and freezing.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl 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/ycw2015-12-19-43/3dimage_71636/</p>20151219_YWC206_10043_part121_5.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20151219_YWC206_10043.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/ycw2015-12-19-43/rawdata/20151219_YWC206_10043.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/a5m-d3q-4d5
title: Siluridae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/metbb-mz595
title: Coxiella_ Verocells_28dpi

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Coxiella cells purified from infected Vero cells.
description: <strong>Tilt Series Date:</strong> 2017-09-25</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</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: 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 sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Refer to Heinzen lab.</p>
<strong>Sample Preparation:</strong> Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.T</p>
  dga2017-09-25-8_slicer18912.jpg: multilayered structure beneath the inner membrane forming also a vesicle.?? dga2017-09-25-8_slicer18913.jpg: multilayered structure beneath the inner membrane dga2017-09-25-8_slicer18914.jpg: non-coxeilla vesicular structures. dga2017-09-25-8_slicer18915.jpg: multilayered strucutre beneath the inner membrane forming a vesicular structure???
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-09-25-8/rawdata/</p>Cb_vero_201709250008.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Cb_vero_201709250008_part61_2.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xfc24-51177
title: wt_perfusion_fixed

description: Raw data files of wt_perfusion_fixed
description: <strong>Tilt Series Date:</strong> 2015-09-19</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: 135.0 eV/Å²,  defocus: -10.0 μm,  magnification: 41000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> The cells look good on scope. Next time use 1.5ul gold.</p>
<strong>Collaborators and Roles:</strong> Moh and Sahand USC</p>
<strong>Purification / Growth Conditions / Treatment:</strong> This sample is wt cells grown in perfusion set-up. It is fixed with 2.5% glutaraldehyde for 15 minutes. The grid was prepared by Sahand on 9/10/15. The grid was triple rinsed in distilled water and saved in distilled water until freezing on 9/15/15 at USC using manual plunger.</p>
<strong>Sample Preparation:</strong> This is gold grid with honey C. The grid was pulled out quickly from media. 1.2ul of 10nm gold was added immediately to the cells on the C side -same side as cells were present. The grid was loaded on manual plunger and blotted from behind- opposite of C side. And then plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2015-09-19-4/3dimage_69603/</p>091915_perfusionwtfixed_sq70004_part121_56.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        091915_perfusionwtfixed_sq70004.mrc,  Tilt Series (Pixel Size 0.26 nm), 3.4 GB  
        
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DOI: 10.5281/zenodo.17010167
title: cleaned data_463_virtual influencer research
DOI: 10.5281/zenodo.17010168
title: cleaned data_463_virtual influencer research
DOI: 10.22002/h81t9-83t72
title: Agro_AD1231

description: AD1231: pAD1361/A136; Carbenicillin 50;  virB, virD4, virGN54D on multicopy plasmid, host lacks a Ti-plasmid. Constitutive virG mutant, does not require AS. But good to have AS in the media, anyway.
description: <strong>Tilt Series Date:</strong> 2015-08-03</p>
<strong>Data Taken By:</strong> Debnath Ghosal</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: 155.0 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> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow culture in AB medium (pH 7) at 30C. For induction, use 375 µl of a decent ON culture to inoculate 5 ml AB mes pH 5.8 medium containing 100 µM Acetosyringone and antibiotic (Cb 50). Grow at 20C for 18 hr. Concentrate cells 5 times by centrifuging. Freeze cells.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK III, MK IV was not working) settings: 100% humidity, 4µl sample, 5% BSA treated gold. Blot offset -5, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
  dga2015-08-03-10_slicer14064.jpg: Chemoreceptor array!
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-08-03-10/3dimage_59999/</p>20150803_1231_10007_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150803_1231_10007.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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DOI: 10.3535/0rb-vv5-hs0
title: †Atrypa Dalman, 1828

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wky-aqk-dcf
title: †Scolymia spinosa (Gerth, 1921)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/3c6sk-8hb55
title: Xanthomonas vs Caulobacter

description: Xac WT pBRaφ pBRR MCS5 GFP (code 9) vs Caulobacter competition
description: <strong>Tilt Series Date:</strong> 2017-03-09</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Xanthomonas citri</p>
<strong>Strain:</strong> pv citri 306</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 160.0 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> Chuck Farah lab made the strains, data collected by Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 4 µL mixture of Xac and Caulobacter cells were pipetted on top of Au-Finder grids. These grids were glow discharged in advance and kept on top of Agar pads. Carbon side up. These were then kept at the BSL-II hood and left for about 10 min before freezing.</p>
<strong>Sample Preparation:</strong> Freezing conditions: Blot force 6, wait time=0, drain time =1 sec, blot time= 10 sec</p>
  dga2017-03-09-18_slicer17976.jpg: t4SS below pore? dga2017-03-09-18_slicer17977.jpg: t4SS? dga2017-03-09-18_slicer17978.jpg: t4ss? dga2017-03-09-18_slicer17979.jpg: t4ss, strange pore forming structure at caulobacter inner membrane ? .   .  4 high density at inner membrane
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-18/rawdata/</p>Xac_Cc_20170309a0018.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-18/rawdata/Xac_Cc_20170309a0018.mrc"
        > <i class="download icon"></i> Download </a></p>

        Xac_Cc_20170309a0018_part61_10.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.2y93kr
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Danio roseus)",
 "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 60 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012059-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k23crv
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus setaceus",
 "Country is Botswana",
 "HasCoordinate is true"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012058-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cgc9uf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus setaceus",
 "Country is Eswatini",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012060-250827131500795/datasets/export for details.
DOI: 10.22002/8mtgm-49243
title: Agro_AD1231

description: AD1231: pAD1361/A136; Carbenicillin 50;  virB, virD4, virGN54D on multicopy plasmid, host lacks a Ti-plasmid. Constitutive virG mutant, does not require AS. But good to have AS in the media, anyway.
description: <strong>Tilt Series Date:</strong> 2015-08-03</p>
<strong>Data Taken By:</strong> Debnath Ghosal</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: 155.0 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> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow culture in AB medium (pH 7) at 30C. For induction, use 375 µl of a decent ON culture to inoculate 5 ml AB mes pH 5.8 medium containing 100 µM Acetosyringone and antibiotic (Cb 50). Grow at 20C for 18 hr. Concentrate cells 5 times by centrifuging. Freeze cells.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK III, MK IV was not working) settings: 100% humidity, 4µl sample, 5% BSA treated gold. Blot offset -5, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
  dga2015-08-03-73_slicer14116.jpg: T6SS
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-08-03-73/3dimage_60121/</p>20150803_1231_20032_part121_57.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150803_1231_20032.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/dga2015-08-03-73/rawdata/20150803_1231_20032.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.6ya8q3
title: Occurrence Download

description: A dataset containing 2411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus setaceus",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2411 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012057-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/hjzcg-n2k37
title: Late stage of dividing cell

description: The final stage of dividing C.crescentus.Septum has formed.No FtsZ ring has been found at the dividing site.
description: <strong>Tilt Series Date:</strong> 2015-02-17</p>
<strong>Data Taken By:</strong> Qing Yao</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: 1.0°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> C. crescentus was from Yi-Wei's cryo-stock and was grown in PYE medium overnight at 30°c 250 rpm. In the next days' morning, 1/20 subculture into the M2G medium. When OD600 reaches 0.48, 1ml medium was spun down and the resuspension was 100 ul for cryo-grid preparation.</p>
<strong>Sample Preparation:</strong> Glow discharged Quantifoil R2/R holey carbon film. 4 ul concentrated gold suspension was added to 16 ul bacteria and mix before plunge freezing. Plunge freezing condition: 6(force)-2(duration time)-1(dry time). Tilt Series Setting: single tilt. constant angular increment, step: 1. tilt range: (-60, 60). dosage: 120/A2. defocus: -10 um. magnification: 22500.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2015-02-17-52/rawdata/</p>ZMatlas20016.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/qya2015-02-17-52/rawdata/ZMatlas20016.mrc"
        > <i class="download icon"></i> Download </a></p>

        ZMatlas20016_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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DOI: 10.3535/yd2-n7j-4ha
title: Eucidaris tribuloides (Lamarck, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1vb-j28-97l
title: Cidaroida Claus, 1880

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.5281/zenodo.17010177
title: Comparison of sample memory effects for vaporizers used in CFA analysis of water isotopes of ice-cores using cavity ring-down spectroscopy

description: Dataset used for analysis and evaluation of signal smoothing. This data is already calibrated using the calibration process described in the manuscript.
DOI: 10.5281/zenodo.17010178
title: Comparison of sample memory effects for vaporizers used in CFA analysis of water isotopes of ice-cores using cavity ring-down spectroscopy

description: Dataset used for analysis and evaluation of signal smoothing. This data is already calibrated using the calibration process described in the manuscript.
DOI: 10.22002/36gmg-30d66
title: Myxococcus xanthus delta-pomXYZ

description: Grid box YWC123(sent to Janelia)
description: <strong>Tilt Series Date:</strong> 2015-05-01</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: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </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> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 10ml cells into 100ml fresh CTT at 30C shaking for 2 days. Resuspend cells with pipet to break up clumps. Spun down 100ml culture in SS-34 rotor for 10 minutes at 5,000rcf. Discard pellet. Spin supernatant for 15 minutes at 30,000rcf.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK vi) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2 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/ycw2015-05-01-15/rawdata/</p>YWC123-B-tomo0004.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        YWC123-B-tomo0004_full.rec,  Reconstruction (Pixel Size 1.68 nm), 516.7 MB  
        
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