cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/tjd49-f7d17
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/scd2018-02-22-6/rawdata/</p>tomography3.mrc,  Tilt Series (Pixel Size 3.26 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2018-02-22-6/rawdata/tomography3.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography3_full.rec,  Reconstruction (Pixel Size 0.0 nm), 1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2018-02-22-6/3dimage_118692/tomography3_full.rec"
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DOI: 10.22002/pwhz4-bpt48
title: H_pylori_dFliO_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliO mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 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 received these cells from Carrie Schaffer from the university of Kentucky. These are wild . . type cells but they don't express complete FliP protein. Therefore, they don't assemble full . . flagella. We knocked out FliO protein of the flagellar motor to study the early assembly states . of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. 10 nm . . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-83/rawdata/</p>Hpylori_FliO_085_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-83/rawdata/Hpylori_FliO_085_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_085_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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DOI: 10.22002/r755r-t0q62
title: E_coli_EPEC_8612

description: The aim is to look for bacterial nanotubes (See Pal et al., 2019 Cell)
description: <strong>Tilt Series Date:</strong> 2020-02-13</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 105.0 eV/Å²,  defocus: -6.0 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> These cells were obtained from Ritesh (Ilan Rosenshine lab) and Amit (Sigal ben Yehuda lab, . both from the Hebrew university). They were present during sample preparation.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> An overnight culture from -80C stock was made in 2ml LB and was grown at 37C in static . conditions. The next day, 1 ml of cells were spun down at 4000 rpm for six minutes and . concentrated 10 times. 3 ul of cells were spotted on glow-discharged grids located on a . DMEM high-glucose agar plates (1.5% agar) for 3 hours. Then, the grids were washed twice . in PBS and transferred to a starvation-medium agar plates (Starvation medium:DMEM without . phenol red, vitamins and amino acids). and incubated for 1 hour at 37C. Subsequently,the . samples were washed with PBS and plunge-frozen. </p>
<strong>Sample Preparation:</strong> The samples were hold with a tweezer from the starvation plates and washed with PBS. Blotted . with different conditions (B</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-13-18/rawdata/</p>EPEC_8612_009_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
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        EPEC_8612_009_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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DOI: 10.15468/dl.uecqkb
title: Occurrence Download

description: A dataset containing 11865 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is one of (February, March, April)",
 "OccurrenceStatus is Present",
 "TaxonKey is Strix nebulosa",
 "Year 1970-2025"
 ]
}

 The dataset includes 11865 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006381-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/vz8cg-36949
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> None</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/mka2019-05-25-2/rawdata/</p>Squ1_2_Montage.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-05-25-2/rawdata/Squ1_2_Montage.mrc"
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        Squ1_2_Montage.mrc.mdoc,  146.7 kB  
        
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DOI: 10.57760/sciencedb.27201
title: Calculation of the energy deposition spectrum in the sensitive region of the device based on in-orbit probe data
title: 器件敏感区域的能量沉积谱基于在轨探测数据的计算

description: This dataset is based on the sedimentary spectra detected by two MEO satellites in orbit, and calculates the sedimentary energy spectrum in the sensitive area of a certain SRAM. This dataset contains three columns, the first column is the sedimentary energy value, and the second and third columns are the sedimentary energy calculated based on M15 satellite detection values (using two calculation methods: A) inversion to LET spectrum and then calculation; Method B: Calculation through Probability Physics Kernel), the fourth and fifth columns show the sedimentary energy calculated based on the M16 satellite detection values.
description: This dataset is based on the sedimentary spectra detected by two MEO satellites in orbit, and calculates the sedimentary energy spectrum in the sensitive area of a certain SRAM. This dataset contains three columns, the first column is the sedimentary energy value, and the second and third columns are the sedimentary energy calculated based on M15 satellite detection values (using two calculation methods: A) inversion to LET spectrum and then calculation; Method B: Calculation through Probability Physics Kernel), the fourth and fifth columns show the sedimentary energy calculated based on the M16 satellite detection values.
DOI: 10.22002/0798z-ca025
title: Hpylori_dFliM

description: These are fast tilt series that I collected on Hpylori_dFliM (dFliP also) on the Titan Krios.
description: <strong>Tilt Series Date:</strong> 2019-11-24</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, 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 received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP . protein. Therefore, they don't assemble full flagella. We knocked out FliM protein of the flagellar motor to study the early assembly states of . flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown for 48 hours and then spread on a new plate with a cotton swab and left to . grow for 24 hours. The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% . humidity. Cu grids. 10 nm gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-24-64/rawdata/</p>Hpylori_dfliM_032_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-24-64/rawdata/Hpylori_dfliM_032_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliM_032_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-24-64/3dimage_110018/Hpylori_dfliM_032_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/skc6w-g5v81
title: Helicobacter_Pylori_dFliO

description: These are H. pylori cells that don't have a complete FliP. In addition, FliO was knocked out in  .  these cells. The aim is to study the assembly of the flagellar motor and the core complex.
description: <strong>Tilt Series Date:</strong> 2019-09-21</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 130.0 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 received these cells from Carrie Schaffer from the university of Kentucky. These are wild . type cells but they don't express complete FliP protein. Therefore, they don't assemble full . flagella. We knocked out FliO protein of the flagellar motor to study the early assembly . . states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1. 100% humidity. Cu grids. 10 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-21-18/rawdata/</p>Hpylori_dFliO_Good50.mrc,  Tilt Series (Pixel Size 0.4494 nm), 2.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-21-18/rawdata/Hpylori_dFliO_Good50.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dFliO_Good50_full.rec,  Reconstruction (Pixel Size 1.7976 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-09-21-18/3dimage_106683/Hpylori_dFliO_Good50_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1zz03-abx79
title: Hpylori_dfliQ

description: These are fast tilt series taken on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-11-19</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 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 received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP protein. Therefore, they don't . assemble full flagella. We knocked out FliQ protein of the flagellar motor to study the early assembly states of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. The cells were grown for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids . were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot, time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. . 10 nm gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-196/rawdata/</p>Hpylori_dfliQ_196_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-11-19-196/rawdata/Hpylori_dfliQ_196_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_196_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/6xs1t-qvj58
title: H_pylori_dFliO_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliO mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-25</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -6.0 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 received these cells from Carrie Schaffer from the university of Kentucky. These are wild . . type cells but they don't express complete FliP protein. Therefore, they don't assemble full . . flagella. We knocked out FliO protein of the flagellar motor to study the early assembly states . of flagellar motor.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . . The grids were prepared from both batches (48 hours, and 24 hours, separately).</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. 10 nm . . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-207/rawdata/</p>Hpylori_FliO_211_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
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        Hpylori_FliO_211_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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