cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/vfg86-acb79
title: non_treated_scale5

description: Raw data files of non_treated_scale5
description: <strong>Tilt Series Date:</strong> 2020-02-12</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Allium cepa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong>  Onion peels generated like Kafle et al. 2013, incubated in HEPES >20min until freezing</p>
<strong>Sample Preparation:</strong> Glow-discharged (15mA – 1min) Quantifoil R2/2 NH2 Cu EM grids (EMSdiasum). Plunge freezing was performed with a 60/40 ratio ethane/propane mix and an FEI Vitrobot Mark IV (Thermo Fisher). Humidity was set at 50%, temperature at 20°C. Grids were first manually backblotted for 6 s in order to attach the cell wall peel firmly to the carbon, followed by two autoblottings (front and back) 5 s, maximal blot force (25) and a drain time of 3 s.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-02-12-1/rawdata/</p>on13-1-3_lam1_ts1.st,  Tilt Series (Pixel Size 0.33 nm), 1.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        on13-1-3_lam1_ts1.hdf,  Reconstruction (Pixel Size 1.32 nm), 1.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        on13-1-3_lam1_ts1.mrc.mdoc,  14.2 kB  
        
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        on13-1-3_lam1_ts1.rawtlt,  200.0 B  
        
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DOI: 10.15468/dl.zjgp9x
title: Occurrence Download

description: A dataset containing 167 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (90fd6680-349f-11d8-aa2d-b8a03c50a862, c54097e6-0972-4acb-b849-eaeba29c917d, 33d232b5-5cc2-4521-8bd6-121c5bb41c32, ef807e08-c954-487f-9e70-3cc75f173812, 8e1a97a0-3ca8-11d9-8439-b8a03c50a862, d0e01e0c-7e8c-49aa-aeed-15fab7dfee46, 7b8aff00-a9f8-11d8-944b-b8a03c50a862, bc092ff0-02e4-11dc-991f-b8a03c50a862, 2e149736-4cc6-44d4-a068-ccb2041baf75)",
 "TaxonKey is Sapindus saponaria"
 ]
}

 The dataset includes 167 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044336-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/09a2n-b6r69
title: Sulfolobus cells synchronized for division

description: search for ESCRT in dividing cells
description: <strong>Tilt Series Date:</strong> 2010-12-04</p>
<strong>Data Taken By:</strong> Megan Dobro</p>
<strong>Species / Specimen:</strong> Sulfolobus acidocaldarius</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 2.7 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </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> grown and synchronized by Rachel Samson in Stephen Bell's lab, Oxford University</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in Brock's Medium at 80C, synchronize with Baby Machine</p>
<strong>Sample Preparation:</strong> frozen at Kay Grunewald's lab. Harrick plasma cleaner. Blotted on both sides, 4 sec, sponge for humidity</p>
  mdj2010-12-04-16_slicer3758.jpg: archaellum mdj2010-12-04-16_slicer3759.jpg: archaellum mdj2010-12-04-16_slicer3760.jpg: archaellum mdj2010-12-04-16_slicer3761.jpg: archaellum  .  basal body? mdj2010-12-04-16_slicer3798.jpg: Sulfolobus acidocaldarius .   .  Dark projection looks like a membrane, with a protein decorated vesicle attached .   .  LR mdj2010-12-04-16_slicer4207.jpg: External vesicle mdj2010-12-04-16_slicer4208.jpg: Granule mdj2010-12-04-16_slicer4211.jpg: Unknown
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2010-12-04-16/rawdata/</p>10dec04b_Box13grid3_016new.mrc,  Tilt Series (Pixel Size 1.258 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mdj2010-12-04-16/rawdata/10dec04b_Box13grid3_016new.mrc"
        > <i class="download icon"></i> Download </a></p>

        10dec04b_Box13grid3_016new_full.rec,  Reconstruction (Pixel Size 2.38 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        mdj2010-12-04-16_slicer19159.png,  REZ .  -andrew, 398.7 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/mdj2010-12-04-16_slicer19159.png"
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        mdj2010-12-04-16_slicer19160.png,  347.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/Caps/mdj2010-12-04-16_slicer19160.png"
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DOI: 10.22002/q8p1k-v4812
title: E.coli co-overexpression

description: E.coli co overexpression UU1607/pJC3/pPM25
description: <strong>Tilt Series Date:</strong> 2013-07-17</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> RP 437</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -3.0 μm,  magnification: 41000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> SIRT</p>
<strong>Collaborators and Roles:</strong> strain sent from Heather Hodges (Kiessling lab), parent strain and plasmids published from the Parkinson lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grew UU1607/pJC3/pPM25 overnight in 5mL TB + 3.8µl Cm + 5µl CarbDiluted back 1:50 into 200mL TB + 152µl Cm + 200µl Carb + 50µl 1M IPTG + 200µl Na-salicylateGrew ~2 hours to mid-log phaseSpun down 10' at 5,000 x gResuspended in 300µl lysis buffer + 0.1µl PMSF + 0.75 µl 1,10-phenanthrolineAdded 33.3µl (2mg/ml) fresh lysozyme solution (20mg/ml in 10mM Tris-HCl, pH 8.0)Incubated 45' at 37°CAdded 1.67µl 1M MgCl2, 0.2µl 1M CaCl2, 0.33µl DNase IIncubated 30' at 37°CSpun down 4000 g 5 min Resuspended in activity buffer (cold room) without glycerol</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-07-17-37/rawdata/</p>cooverexpressionatlas4micronmin30sanglesa.mrc,  Tilt Series (Pixel Size 0.28 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-07-17-37/rawdata/cooverexpressionatlas4micronmin30sanglesa.mrc"
        > <i class="download icon"></i> Download </a></p>

        cooverexpressionatlas4micronmin30sanglesaSIRTrot.rec,  Reconstruction (Pixel Size 0.0 nm), 11.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        cooverexpressionatlas4micronmin30sanglesa.rec,  Reconstruction (Pixel Size 0.0 nm), 3.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        cooverexpressionatlas4micronmin30sanglesaSIRT.rec,  Reconstruction (Pixel Size 0.0 nm), 12.8 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.7dqvmu
title: Occurrence Download

description: A dataset containing 3203 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Enneapogon desvauxii"
 ]
}

 The dataset includes 3203 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044333-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/0ytff-94638
title: A413T cooverexpression

description: co overexpression strain UU1607/pJC3/pPM25  with A413T mutation in tsr (mutation made by Cathereine, strain and plasmids published. Sent from Heather Hodges (Kiessling lab)
description: <strong>Tilt Series Date:</strong> 2013-08-30</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> RP 437</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: -10.0 μm,  magnification: 34000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Laura Kiessling</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grew UU1607/pJC3/pPM25 overnight in 5mL TB + 3.8µl Cm + 5µl CarbDiluted back 1:50 into 200mL TB + 152µl Cm + 200µl Carb + 50µl 1M IPTG + 200µl Na-salicylateGrew ~2 hours to mid-log phaseSpun down 10' at 5,000 x gResuspended in 300µl lysis buffer + 0.1µl PMSF + 0.75 µl 1,10-phenanthrolineAdded 33.3µl (2mg/ml) fresh lysozyme solution (20mg/ml in 10mM Tris-HCl, pH 8.0)Incubated 45' at 37°CAdded 1.67µl 1M MgCl2, 0.2µl 1M CaCl2, 0.33µl DNase IIncubated 30' at 37°CSpun down 4000 g 5 min Resuspended in activity buffer (cold room) without glycerol</p>
  aba2013-08-30-3_slicer9493.jpg: E. coli .  vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-08-30-3/rawdata/</p>A413tCoover0003.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/aba2013-08-30-3/rawdata/A413tCoover0003.mrc"
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        A413tCoover0003.rec,  Reconstruction (Pixel Size 0.0 nm), 1.2 GB  
        
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        A413tCoover0003SIRTrot.rec,  Reconstruction (Pixel Size 0.0 nm), 4.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-08-30-3/3dimage_46533/A413tCoover0003SIRTrot.rec"
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        nadA413tCoover0003SIRTrot.rec,  Reconstruction (Pixel Size 0.0 nm), 4.8 GB  
        
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DOI: 10.22002/sx6na-rz989
title: Alongum

description: Alongum_lysozyme
description: <strong>Tilt Series Date:</strong> 2012-05-20</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-30.0°, 30.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> WesleyChen helped remove layers</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/etl2012-05-20-98/rawdata/</p>ecolilys0003.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-98/rawdata/ecolilys0003.mrc"
        > <i class="download icon"></i> Download </a></p>

        ecolilys0003_full.rec,  Reconstruction (Pixel Size 1.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/34j6m-znv67
title: Alongum

description: Alongum_noOM
description: <strong>Tilt Series Date:</strong> 2012-05-20</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-30.0°, 30.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> WesleyChen helped remove layers</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/etl2012-05-20-112/rawdata/</p>ecoliNoOM0006.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-112/rawdata/ecoliNoOM0006.mrc"
        > <i class="download icon"></i> Download </a></p>

        ecoliNoOM0006_part122_4.rec,  Reconstruction (Pixel Size 1.95 nm), 4.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-112/3dimage_56941/ecoliNoOM0006_part122_4.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dgkt8-a2c83
title: Alongum

description: Alongum_lysozyme
description: <strong>Tilt Series Date:</strong> 2012-05-20</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-30.0°, 30.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> WesleyChen helped remove layers</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/etl2012-05-20-104/rawdata/</p>ecolilys20005.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-104/rawdata/ecolilys20005.mrc"
        > <i class="download icon"></i> Download </a></p>

        ecolilys20005_full.rec,  Reconstruction (Pixel Size 1.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.7910/dvn/m9wpnr
title: Data for Emergent Neural Network Mechanisms for Generalization to Objects in Novel Orientations

description: This dataset contains the data for the study: "Emergent Neural Network Mechanisms for Generalization to Objects in Novel Orientations"
DOI: 10.22002/e8e52-v5s82
title: Alongum

description: Alongum_protK
description: <strong>Tilt Series Date:</strong> 2012-05-20</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-30.0°, 30.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> WesleyChen helped remove layers</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/etl2012-05-20-128/rawdata/</p>ecoliProtK0007.mrc,  Tilt Series (Pixel Size 0.95 nm), 842.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-128/rawdata/ecoliProtK0007.mrc"
        > <i class="download icon"></i> Download </a></p>

        ecoliProtK0007_part102_21.rec,  Reconstruction (Pixel Size 1.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2012-05-20-128/3dimage_56973/ecoliProtK0007_part102_21.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6s5g9-z5f68
title: Vibrio fischeri

description: Session notes: Vibrio fischeri WT flagella, binned 4x total then filtered 0.28 (= 4.6nm resolution cutoff) Tilt series notes:  Tomogram notes:
description: <strong>Tilt Series Date:</strong> 2011-12-17</p>
<strong>Data Taken By:</strong> Morgan Beeby</p>
<strong>Species / Specimen:</strong> Vibrio fischeri</p>
<strong>Strain:</strong> ES114</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: 10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
  mba2011-12-17-25_slicer6485.jpg: chemoreceptor mba2011-12-17-25_slicer6487.jpg: flagellar motor (two) mba2011-12-17-25_slicer6488.jpg: peptidoglycan
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mba2011-12-17-25/rawdata/</p>11dec17c_WTVFischeri_0015.st,  Tilt Series (Pixel Size 0.632 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        11dec17c_WTVFischeri_0015.rec,  Reconstruction (Pixel Size 0.644 nm), 170.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dnra3-j3z30
title: Alongum

description: Alongum_protK
description: <strong>Tilt Series Date:</strong> 2012-05-20</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-30.0°, 30.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> WesleyChen helped remove layers</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/etl2012-05-20-135/rawdata/</p>ecoliProtK0015.mrc,  Tilt Series (Pixel Size 0.95 nm), 842.5 MB  
        
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        ecoliProtK0015_part102_83.rec,  Reconstruction (Pixel Size 1.95 nm), 1.0 GB  
        
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