cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/me1sg-y1365
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-44/rawdata/</p>P_aeruginosa_DfliP8.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-44/rawdata/P_aeruginosa_DfliP8.mrc"
        > <i class="download icon"></i> Download </a></p>

        P_aeruginosa_DfliP8_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        P_aeruginosa_DfliP8.mrc.mdoc,  31.1 kB  
        
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DOI: 10.22002/08a3e-v4n97
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-18/rawdata/</p>P_aeruginosa_DfliP32.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
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        P_aeruginosa_DfliP32_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        P_aeruginosa_DfliP32.mrc.mdoc,  32.2 kB  
        
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DOI: 10.22002/ha6v1-04s75
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-21/rawdata/</p>P_aeruginosa_DfliP21.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        P_aeruginosa_DfliP21_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        P_aeruginosa_DfliP21.mrc.mdoc,  32.2 kB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.supwhc
title: Occurrence Download

description: A dataset containing 1949 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea japonica",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1949 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002705-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/r3x6q-ap885
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-37/rawdata/</p>P_aeruginosa_DfliP42.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-37/rawdata/P_aeruginosa_DfliP42.mrc"
        > <i class="download icon"></i> Download </a></p>

        P_aeruginosa_DfliP42_part61_13.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        P_aeruginosa_DfliP42.mrc.mdoc,  32.2 kB  
        
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DOI: 10.15468/dl.tdptc2
title: Occurrence Download

description: A dataset containing 242 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is one of (Africa, Europe)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex depressa"
 ]
}

 The dataset includes 242 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002706-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/91hj8-fnk77
title: IRE1α mNeon-Green MEF

description: cryo-CLEM
description: <strong>Tilt Series Date:</strong> 2018-02-22</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> Mouse Embryonic Fibroblasts</p>
<strong>Strain:</strong> IRE1α-mNeonGreen stable expression</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, 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> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Peter Walter</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Prior to cell plating, gold Quantifoil London finder grids (EMS R2/2 LF-Au-NH2) were UV treated to sterilize and coated with cell adhesion matrix. For MEFs-IRE1-mNG cell line, grids were coated in droplets of 500 ug/mL Fibronectins (Sigma-Aldrich S5171-.5MG) for 5 minutes on each side, washed in PBS, blotted and air-dried. For U2OS-IRE1-mNG cell line, grids were coated with ~4 mg/mL undiluted Collagen type I (Corning 354236) droplets for 20 minutes, washed in PBS, blotted and air-dried. Cells were seeded at 15% confluence and allowed to adhere for 8 hours and induced with Doxycycline (500 nM) for 6 or 18 hours for MEFs and U-2 OS cell lines, respectively. ER stress was then induced by treatment with 1.5 ug/mL of Tunicamycin for 2 hours.</p>
<strong>Sample Preparation:</strong> Manual Blotting</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2018-02-22-9/rawdata/</p>tomography5.mrc,  Tilt Series (Pixel Size 3.26 nm), 3.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        sirt.rec,  Reconstruction (Pixel Size 0.0 nm), 2.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2018-02-22-9/3dimage_118693/sirt.rec"
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        tomography5_full.rec,  Reconstruction (Pixel Size 0.0 nm), 668.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2018-02-22-9/3dimage_118694/tomography5_full.rec"
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DOI: 10.22002/qm1ac-c9520
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-10/rawdata/</p>P_aeruginosa_DfliP30.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-10/rawdata/P_aeruginosa_DfliP30.mrc"
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        P_aeruginosa_DfliP30_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        P_aeruginosa_DfliP30.mrc.mdoc,  32.1 kB  
        
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DOI: 10.22002/yxgwq-p3h95
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-3/3dimage_103295/</p>P_aeruginosa_DfliP36_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        P_aeruginosa_DfliP36.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.9 GB  
        
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        P_aeruginosa_DfliP36.mrc.mdoc,  32.2 kB  
        
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DOI: 10.22002/cg8zs-5r710
title: Pseudomonas_aeruginosa_DfliP

description: This sample was imaged to check for the presence of the tentative flagellar inner-membrane- .  embedded structures in FliP knockout
description: <strong>Tilt Series Date:</strong> 2019-05-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newman lab from the transposon library (mutant 10239 from . the full library excel file). Shannon Park helped me to get the cells.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were first grown on LB plate with 100 ug/ml gentamicin over night (from -80 C stock). . Next dat, one colony was inoculated in 2 ml of LB (with 100 ug/ml gentamicin) and incubated . for 16 hours at 37 C with 175 rpm. After cells were mixed with gold beads (coated with BSA), . 4 ul were added to the grids, blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> Different plunge-freezing parameters: 1) blot force 6, blot time 3s, drain time 1s. 2) blot force 3, . blot time 2s, drain time 1s. 3) blot force -5, blot time 4s, drain time 1s. 4) blot force -3, blot time . 2s, drain time 1s. All conditions were at room temperature with 100 % humidity.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-7/3dimage_103303/</p>P_aeruginosa_DfliP11_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        P_aeruginosa_DfliP11.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.8 GB  
        
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        P_aeruginosa_DfliP11.mrc.mdoc,  31.6 kB  
        
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