cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/34pzd-syt53
title: AD348_delVirB_Agro

description: Mutant Agro cells, delVirB (whole of the VirB system deleted). Grown on induction plate pH5.8 in exactly similar way as the AD1484 strain.
description: <strong>Tilt Series Date:</strong> 2016-01-06</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: 160.0 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 at 19C for 4 days on induction plate. Add 400 ul of induction media to one of the induction plates (containing lawn of Agrobacterium AD348_delVirB) and wash the plate by gently rolling the liquid. Add gold to this: 1ul of gold to 4 ul of cells, freeze.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 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/dga2016-01-06-2/3dimage_72360/</p>AD348_delVirB0002.rec,  Reconstruction (Pixel Size 19.2 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-06-2/3dimage_72360/AD348_delVirB0002.rec"
        > <i class="download icon"></i> Download </a></p>

        AD348_delVirB0002.mrc,  Tilt Series (Pixel Size 4.8 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-06-2/rawdata/AD348_delVirB0002.mrc"
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DOI: 10.3535/ag6-0tb-wwm
title: Coleoidea Bather, 1888

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/laz-y33-4kq
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mek-g15-68n
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qyy-ag2-as1
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rt0-rd9-bc7
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/2zk9n-n3w33
title: Agro_piliprep7_highmag_16.09.15

description: AD1484:A348dB/pAD2079, virB on a multicopy-plasmidFor pili prep, following buffer was used: 20 mM Tris-HCl, pH 7.8, 100 mM NaCl and 0.5% deoxycholate.Did not add any gold. I assumed we will only do high resolution imaging. However, later we decided to do tomography and used patch tracking to process the data. Grids were little contaminated and data is not very high quality.
description: <strong>Tilt Series Date:</strong> 2015-09-16</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: 120.0 eV/Å²,  defocus: -10.0 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> Patch Tracking</p>
<strong>Collaborators and Roles:</strong> Pili prep from induced strain (AD1484) was done by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline. This data was collected at the F30, Caltech.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> For pili prep, following buffer was used: 20 mM Tris-HCl, pH 7.8, 100 mM NaCl and 0.5% deoxycholate.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: incubate at 100% humidity for at least 15 min, 4µl sample, blot force 6, blot time 3 sec. Wait time 30 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Did not add any gold. I assumed we will only do high resolution imaging. However, later we decided to do tomography and used patch tracking to process the data.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-09-16-10/rawdata/</p>AD1484_piliprep70009.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-09-16-10/rawdata/AD1484_piliprep70009.mrc"
        > <i class="download icon"></i> Download </a></p>

        AD1484_piliprep70009.rec,  Reconstruction (Pixel Size 1.28 nm), 890.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/d1g-7b2-vy2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2xj-jxj-pab
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4d5-1x0-ccp
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m7h-199-qzy
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8dy-320-ztc
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cfs-nfj-a82
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/e1ceh-ypr72
title: AD348_delVirB_Agro

description: Mutant Agro cells, delVirB (whole of the VirB system deleted). Grown on induction plate pH5.8 in exactly similar way as the AD1484 strain.
description: <strong>Tilt Series Date:</strong> 2016-01-06</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: 160.0 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 at 19C for 4 days on induction plate. Add 400 ul of induction media to one of the induction plates (containing lawn of Agrobacterium AD348_delVirB) and wash the plate by gently rolling the liquid. Add gold to this: 1ul of gold to 4 ul of cells, freeze.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 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 ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-06-30/3dimage_72229/</p>AD348_delVirB_5th-atlas0001.rec,  Reconstruction (Pixel Size 19.2 nm), 890.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        AD348_delVirB_5th-atlas0001.mrc,  Tilt Series (Pixel Size 4.8 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-06-30/rawdata/AD348_delVirB_5th-atlas0001.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/75e9x-qyr76
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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-08-03-16/3dimage_60015/</p>20150803_1231_10013_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_10013.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/dga2015-08-03-16/rawdata/20150803_1231_10013.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/97a0n-1bj12
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: -6.0 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/psa2015-09-19-15/3dimage_69625/</p>091915_perfusionwtfixed_sq70015_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        091915_perfusionwtfixed_sq70015.mrc,  Tilt Series (Pixel Size 0.26 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.2dzq5y
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus madritensis",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011967-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wvnkd5
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Inula acuminata"
 ]
}

 The dataset includes 72 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011969-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/arx82-ezh73
title: Coxiella_burnetii_ wtACCMD_pH4d5

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-5 culture. Cells grown in acidic media ACCMD and pH 4.75
description: <strong>Tilt Series Date:</strong> 2017-08-15</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> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab. 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.</p>
  dga2017-08-15-31_slicer18746.jpg: long filaments in the cytoplasm dga2017-08-15-31_slicer18747.jpg: long filaments in the cytoplasm dga2017-08-15-31_slicer18748.jpg: vesicle in the cytoplasm
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-08-15-31/rawdata/</p>Cb_20170816_Cb1pH4d50030.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Cb_20170816_Cb1pH4d50030_part61_6.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.phmhja
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus madritensis",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011970-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/97ak9-s6v49
title: AD348_delVirB_Agro

description: Mutant Agro cells, delVirB (whole of the VirB system deleted). Grown on induction plate pH5.8 in exactly similar way as the AD1484 strain.
description: <strong>Tilt Series Date:</strong> 2016-01-06</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: 160.0 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 at 19C for 4 days on induction plate. Add 400 ul of induction media to one of the induction plates (containing lawn of Agrobacterium AD348_delVirB) and wash the plate by gently rolling the liquid. Add gold to this: 1ul of gold to 4 ul of cells, freeze.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 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 ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-06-71/3dimage_72289/</p>AD348_delVirB_7th-atlasTile010021.rec,  Reconstruction (Pixel Size 19.2 nm), 890.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        AD348_delVirB_7th-atlasTile010021.mrc,  Tilt Series (Pixel Size 4.8 nm), 3.4 GB  
        
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DOI: 10.22002/b5kyj-sxz84
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>
  dga2017-03-09-26_slicer17990.jpg: calobater S layer- Xac interaction interface  .  Xac 20nm t4SS?? dga2017-03-09-26_slicer17991.jpg: t4SS? dga2017-03-09-26_slicer17992.jpg: fiber like structrure? 25nm
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-03-09-26/rawdata/</p>Xac_Cc_20170309a0030.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        Xac_Cc_20170309a0030_part61_20.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/vwh-0b7-qgv
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.bme8aa
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bromus madritensis",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011968-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.