cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/jv7vs-r8c53
title: JV7967

description: Legionella thyA ΔdotI ΔdotJ
description: <strong>Tilt Series Date:</strong> 2016-08-11</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV7967 strain at OD~3.3. 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. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-64/rawdata/</p>JV79670041.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-64/rawdata/JV79670041.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV79670041_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV79670041.tlt,  624.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-64/file_25235/JV79670041.tlt"
        > <i class="download icon"></i> Download </a></p>

        T2SSK.mod,  1.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-64/file_25236/T2SSK.mod"
        > <i class="download icon"></i> Download </a></p>

        T2SSK_2k.mod,  1.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-64/file_25237/T2SSK_2k.mod"
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DOI: 10.22002/a61n2-fnp05
title: JV5460

description: JV5460 Legionella (Superdeletion+CDH)
description: <strong>Tilt Series Date:</strong> 2016-08-13</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 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> reupload_downloaded</p>
<strong>Processing Software Used:</strong> TOMO3D</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate and cysteine hydrochloride (no thymidine). Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV5460 strain at OD~2.9. 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. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-13-18/rawdata/</p>atlas10009.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-13-18/rawdata/atlas10009.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas10009_SIRT_1k.rec,  Reconstruction (Pixel Size 0.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-13-18/3dimage_108458/atlas10009_SIRT_1k.rec"
        > <i class="download icon"></i> Download </a></p>

        atlas10009.tlt,  592.0 B  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-13-18/file_25275/atlas10009.tlt"
        > <i class="download icon"></i> Download </a></p>

        T2SSK.mod,  1.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-13-18/file_25276/T2SSK.mod"
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        T2SSK_2k.mod,  1.1 kB  
        
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DOI: 10.22002/pfqxw-tsv79
title: Cthermocellum4_d3

description: glu+oat spelt xylan
description: <strong>Tilt Series Date:</strong> 2015-05-10</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Clostridium thermocellum</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: 18000x. </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> Eric Matson</p>
  etl2015-05-10-9_slicer20021.jpg: 46 nm cell-bound cellulosome? - Nicholas etl2015-05-10-9_slicer20022.jpg: 46 nm cell-bound cellulosome? - Nicholas
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2015-05-10-9/rawdata/</p>Cthermo4_d30005.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Cthermo4_d30005_full.rec,  Reconstruction (Pixel Size 2.4 nm), 712.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        etl2015-05-10-9_slicer16406.png,  REZ or reconstruction artifact? .  Rectangular dot pattern extends deep into the cell an resembles filaments in the Z direction when viewed sideways.  (See other snapshot.)  Spacing in the Y direction is 3.2pixels (77nm) .  -Andrew, 263.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/etl2015-05-10-9_slicer16406.png"
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        etl2015-05-10-9_slicer16401.png,  295.4 kB  
        
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        etl2015-05-10-9_slicer16400.png,  222.5 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.vjqtnk
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chile",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Stellaria media"
 ]
}

 The dataset includes 123 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033100-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wze2su
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Corydoras nanus)",
 "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 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033102-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/be9wr-7w367
title: Skinny E. coli with GFP-MreB

description: Raw data files of Skinny E. coli with GFP-MreB
description: <strong>Tilt Series Date:</strong> 2010-03-05</p>
<strong>Data Taken By:</strong> Zhuo Li</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: 1.5°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR and Peach</p>
<strong>Collaborators and Roles:</strong> Skinny E. coli (DS664) and plasmids pDS176 (gfp-mreB in pKG116) and pDS728 (gfp-mreB-A125V in pKG116) were provided by Daisuke Shiomi. Plasmids were transformed into DS664 by electroporation by Zhuo Li. Data collected and processed by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> L broth. GFP-MreB was induced by salicylate. For correlative LM and ECT, membrane dye FM4-64 was added (001-012)</p>
<strong>Sample Preparation:</strong> R2/2 CF or Quantifoil, 10 nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-03-05-10/rawdata/</p>10mar05a_corr_gm_J_010.mrc,  Tilt Series (Pixel Size 1.192 nm), 721.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10mar05a_corr_gm_J_010_full.rec,  Reconstruction (Pixel Size 2.384 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe2_010.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe2_010_part.rec,  Reconstruction (Pixel Size 2.384 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        zla2010-03-05-10_slicer19208.png,  718.7 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/zla2010-03-05-10_slicer19208.png"
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DOI: 10.15468/dl.qz86xm
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033103-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/wxygv-qny71
title: E.cloacae-typeV-CdiA+

description: Type V secretion system
description: <strong>Tilt Series Date:</strong> 2014-03-03</p>
<strong>Data Taken By:</strong> Poorna Subramanian</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: 190.0 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>Collaborators and Roles:</strong> Drs. Davod Low and Chris Hayes, UC Santa Barbara</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grew 2 ml LB culture from stock with Amp 150, Cm 100 till OD ~0.55, induced with 1.5mM IPTG and grown for 4h, then freeze as such, no spinning</p>
<strong>Sample Preparation:</strong> Blot time 3s, Blot off-set -4, 3 ul culture</p>
  psa2014-03-03-11_slicer10295.jpg: unknown, Enterobacter cloacae
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2014-03-03-11/rawdata/</p>atlas10011.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/psa2014-03-03-11/rawdata/atlas10011.mrc"
        > <i class="download icon"></i> Download </a></p>

        atlas10011_part121_5.rec,  Reconstruction (Pixel Size 1.92 nm), 801.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2014-03-03-11/3dimage_39534/atlas10011_part121_5.rec"
        > <i class="download icon"></i> Download </a></p>

        psa2014-03-03-11_slicer19214.png,  irregularly shaped REZ .  (E.cloacae-typeV-CdiA+)  Cell was grown in Amp150 with 1.5nM IPTG.  Cell looks somewhat sickly.  -andrew, 937.3 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/psa2014-03-03-11_slicer19214.png"
        > <i class="download icon"></i> Download </a></p>

        psa2014-03-03-11_slicer19215.png,  inclusion bodies ? .  ( nuages ) .  -andrew, 493.2 kB  
        
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        psa2014-03-03-11_slicer19356.png,  1.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/psa2014-03-03-11_slicer19356.png"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ff8y5q
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033104-250811113504898/datasets/export for details.
DOI: 10.22002/519d7-fg276
title: Treponema primitia

description: Treponema primitia.  The rest of the files are in ~/Images/050911ribosome exclusion zone, REZ, possible visible nucleoid
description: <strong>Tilt Series Date:</strong> 2005-09-11</p>
<strong>Data Taken By:</strong> Gavin Murphy</p>
<strong>Species / Specimen:</strong> Treponema primitia</p>
<strong>Strain:</strong> ZAS-2</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 30.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Microscope:</strong> 0</p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> Cells provided by Eric Matson, Jared Leadbetter; Data collected and processed by Gavin Murphy</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown in standard media around exponential growth.  Removed from anaerobic tube with syringe. Uncentrifuged.</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
  T3_050911_tilt.jpg: * associated to rawdata T3_050911_rec.jpg: file associated to 3D Image #50 T3_050911_seg.jpg: file associated to 3D Image #50 gme2005-09-11-3_slicer9518.jpg: Treponema primitia .  pili bundle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gme2005-09-11-3/rawdata/</p>T3_S552G2_18kx14d130e.mrc.gz,  Tilt Series (Pixel Size 0.98 nm), 850.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        T3B2s.mrc,  Reconstruction (Pixel Size 0.0 nm), 248.3 MB  
        
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        T3B2sBB_24_part.pif,  Reconstruction (Pixel Size 0.0 nm), 443.9 kB  
        
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        > <i class="download icon"></i> Download </a></p>

        T3_050911_seg.tif,  file associated to 3D Image #50, 634.9 kB  
        
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        gme2005-09-11-3_slicer14133.png,  ribosome exclusion zone (REZ) contains faint flow-lines resembling patterns seen in condensed nucleoids. -Andrew, 309.5 kB  
        
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DOI: 10.15468/dl.vytcrw
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudosuccinea columella",
 "Country is New Zealand",
 "HasCoordinate is true"
 ]
}

 The dataset includes 50 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033101-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/qchcr-k1p36
title: Caulobacter crescentus

description: wild type CB15N. 7 of 7, some warping in lower-right quadrant, good contrast. skinny straight swarmer? cell; no obvious S-layer; no obvious filaments; amorphous medium-dense core without ribosomes, ~1/3 cell length; >5 very small storage granules
description: <strong>Tilt Series Date:</strong> 2006-09-20</p>
<strong>Data Taken By:</strong> Prabha Dias</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.6°, 60.6°), step: 0.7°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Microscope:</strong> 0</p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> specimen prep, data collection & processing: D. Prabha Dias</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ddi-water ATCC (PYE) media;  cultured in 50ml flask; 7 days growth; see DPD notebook Sep 13-18, 2006</p>
<strong>Sample Preparation:</strong> box 697, grid 3; MeOH-washed Quantifoil R2/1; 10nm gold on grids & in suspension; offset -2, blot 1.5 sec, drain 1 sec; see DPD notebook Sep 18, 2006</p>
  SAVE_06Sep20t07_xy.jpg: file associated to 3D Image #341 pdd2006-09-20-7_slicer10065.jpg: Caulobacter crescentus .  REZ ribosome exclusion zone
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/pdd2006-09-20-7/rawdata/</p>CC06Sep20t07.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.5 GB  
        
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        CC06Sep20t07_18kx.mrc,  Tilt Series (Pixel Size 1.2 nm), 8.4 MB  
        
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        06Sep20t07bn_full.rec,  Reconstruction (Pixel Size 2.4 nm), 734.0 MB  
        
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        SAVE_06Sep20t07_xy.tif,  file associated to 3D Image #341, 2.9 MB  
        
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        06Sep20t07.mov,  file associated to 3D Image #341, 373.4 MB  
        
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