cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/sw2qh-8f684
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/mka2019-10-25-129/rawdata/</p>Hpylori_FliO_131_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/mka2019-10-25-129/rawdata/Hpylori_FliO_131_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_131_af_part39_3.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/mka2019-10-25-129/3dimage_107494/Hpylori_FliO_131_af_part39_3.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/vh77a-pgk37
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/mka2020-02-13-87/rawdata/</p>EPEC_8612_101_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/mka2020-02-13-87/rawdata/EPEC_8612_101_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_101_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/mka2020-02-13-87/3dimage_110987/EPEC_8612_101_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7c6gs-5nj75
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/mka2019-11-24-63/rawdata/</p>Hpylori_dfliM_078_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/mka2019-11-24-63/rawdata/Hpylori_dfliM_078_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliM_078_af_part41_1.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/mka2019-11-24-63/3dimage_110003/Hpylori_dfliM_078_af_part41_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/j7t-zcv-4m7
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/b9vhn-adb84
title: lip10-2 (+ megacomplex)

description: Exposure 1-1.3s
description: <strong>Tilt Series Date:</strong> 2020-09-29</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> PK2, BL21 dHisdHA RQABpCDF+EFGpRSF</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 56.0 eV/Å²,  defocus: -8.0 μm,  magnification: 11000x. </p>
<strong>Microscope:</strong> IECB Talos Artica</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> Petya Krasteva (head of the SBB lab at the IECB, Bordeaux° and Wiem . Abidi (graduate student) did the preps and helped with acquisition</p>
<strong>Purification / Growth Conditions / Treatment:</strong> BL21 cells were transformed with QAB - pCDF plasmid and EFG - pRSF . plasmid to express the inner-membrane macro-complex.. . Selection done with Kanamycin and Streptomycin.. . Induction of expression ON done with IPTG. . Spheroplasts are generated from the BL21 non transformed cells cells.. Spheroplasts are processed through a high-pressure homogenizer and . further purification by ultracentrifugation of the membrane . fractions. . Liposomes are then generated from the membrane fractions by . processing through Potter and sonicator.. </p>
<strong>Sample Preparation:</strong> Fiducials were prepared my method (see lab archive). . Grids: Quantifoil Cu NH2 R2/2. . Glowdischarged 3mA - 2min. BT3s - BF0. 4uL pipetted on the grids</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-09-29-37/rawdata/</p>lip10-2-sq3-tg13.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-09-29-37/rawdata/lip10-2-sq3-tg13.mrc"
        > <i class="download icon"></i> Download </a></p>

        lip10-2-sq3-tg13_full.rec,  Reconstruction (Pixel Size 0.78 nm), 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2020-09-29-37/3dimage_115804/lip10-2-sq3-tg13_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/pns-8ws-7e4
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/cy4qw-dvz63
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/mka2019-10-25-200/rawdata/</p>Hpylori_FliO_203_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-200/rawdata/Hpylori_FliO_203_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_203_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/mka2019-10-25-200/3dimage_107634/Hpylori_FliO_203_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/g7dps-t8t78
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/mka2019-11-19-191/rawdata/</p>Hpylori_dfliQ_191_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/mka2019-11-19-191/rawdata/Hpylori_dfliQ_191_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_191_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/mka2019-11-19-191/3dimage_109059/Hpylori_dfliQ_191_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ne4zzd
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus setaceus",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012078-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/7y2zz-q1r25
title: H-pylori_dFliM_GC

description: These are fast tilt series taken by Georges Chreifi on the Krios for dFliM mutant of Helicobacter  .  pylori.
description: <strong>Tilt Series Date:</strong> 2019-10-28</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 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/mka2019-10-28-118/rawdata/</p>Hpylori_FliM_120_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-28-118/rawdata/Hpylori_FliM_120_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_120_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/mka2019-10-28-118/3dimage_107912/Hpylori_FliM_120_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/52r-rgp-2lj
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c67-mv4-hp7
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/twn-6rj-8cv
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/rqpwf-ayf35
title: IRE1α mNeon-Green USOS

description: cryo-CLEM
description: <strong>Tilt Series Date:</strong> 2018-10-15</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> U2OS cells</p>
<strong>Strain:</strong> IRE1α-mNeonGreen 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> Undefined</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/scd2018-10-15-9/rawdata/</p>tomography8.mrc,  Tilt Series (Pixel Size 6.52 nm), 824.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2018-10-15-9/rawdata/tomography8.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography8_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/scd2018-10-15-9/3dimage_118708/tomography8_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/0qv-2vs-2sc
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/es8-800-f9g
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mme-r4f-mdx
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r7z-p4s-ae4
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5s1-aee-ha2
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zbh-h8z-01g
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.