cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/74sdm-a2k30
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/wnj2020-09-29-43/rawdata/</p>lip10-2-sq3-tg11.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/wnj2020-09-29-43/rawdata/lip10-2-sq3-tg11.mrc"
        > <i class="download icon"></i> Download </a></p>

        lip10-2-sq3-tg11_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/wnj2020-09-29-43/3dimage_115811/lip10-2-sq3-tg11_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9zy30-y5m06
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/mka2019-10-28-70/rawdata/</p>Hpylori_FliM_072_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/mka2019-10-28-70/rawdata/Hpylori_FliM_072_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliM_072_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/mka2019-10-28-70/3dimage_107817/Hpylori_FliM_072_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/94tbc-73h05
title: Ecoli_EPEC_8612

description: Bacterial nanotubes as described by the work of Ilan Rosenshine and Sigal Ben Yehuda labs at  .  the Hebrew university).
description: <strong>Tilt Series Date:</strong> 2020-02-14</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: 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> 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/mka2020-02-14-44/rawdata/</p>EPEC_8612_189_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/mka2020-02-14-44/rawdata/EPEC_8612_189_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_189_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/mka2020-02-14-44/3dimage_111131/EPEC_8612_189_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/jfw0c-0h525
title: E_coli_EPEC_8770

description: This is to look for bacterial nanotubes. These cells were imaged previously with U2OS cells and  .  no tubes were found. They are imaged alone here to see if they form nanotubes without U2OS. .  They lack the conjugation pilus, the Bundle-forming pilus but they have the core.
description: <strong>Tilt Series Date:</strong> 2020-02-26</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8770, EPEC 8612 + Δbfp ΔtraD-ygeB ΔfinO-traI</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 115.0 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> Samples were prepared with Amit and Ritesh (from Ilan Rosenshine and Sigal ben Yehuda labs . at the Hebrew university)</p>
<strong>Purification / Growth Conditions / Treatment:</strong> An overnight culture from a pre-prepared agar LB plate 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> Samples were washed with PBS before blotting. Subsequently, the samples were automatically . blotted and plunge-frozen</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-26-147/rawdata/</p>EPEC_8770_001.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/mka2020-02-26-147/rawdata/EPEC_8770_001.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8770_001_part41_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/mka2020-02-26-147/3dimage_111994/EPEC_8770_001_part41_3.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1hedn-dtd29
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/mka2019-10-25-190/rawdata/</p>Hpylori_FliO_193_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/mka2019-10-25-190/rawdata/Hpylori_FliO_193_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_193_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/mka2019-10-25-190/3dimage_107616/Hpylori_FliO_193_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/n8njr-jmv60
title: Hpylori_dflgS

description: These are H. pylori cells that don't have a complete FliP. In addition, FlgS 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> 2019-11-23</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 FlgS 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/mka2019-11-23-70/rawdata/</p>Hpylori_dflgS_022_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/mka2019-11-23-70/rawdata/Hpylori_dflgS_022_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dflgS_022_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/mka2019-11-23-70/3dimage_109570/Hpylori_dflgS_022_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/x1htb-gjq93
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/mka2019-10-25-169/rawdata/</p>Hpylori_FliO_172_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-10-25-169/rawdata/Hpylori_FliO_172_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_172_af_part40_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/mka2019-10-25-169/3dimage_107572/Hpylori_FliO_172_af_part40_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.pvgnph
title: Occurrence Download

description: A dataset containing 1287667 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Noctua pronuba"
 ]
}

 The dataset includes 1287667 records from 865 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006393-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nmsk86
title: Occurrence Download

description: A dataset containing 590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Forsterygion varium",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 590 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005571-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fjqdja
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aplocheilichthys lacustris, Lacustricola lacustris, Aplocheilichthys macrurus, Lacustricola macrurus, Aplocheilichthys maculatus, Lacustricola maculatus, Aplocheilichthys mediolateralis, Lacustricola mediolateralis, Aplocheilichthys nigrolateralis, Lacustricola nigrolateralis, Aplocheilichthys omoculatus, Lacustricola omoculatus, Aplocheilichthys rudolfianus, Micropanchax rudolfianus, Aplocheilichthys spilauchen, Aplocheilichthys usanguensis, Lacustricola usanguensis, Aplocheilichthys vitschumbaensis, Lacustricola vitschumbaensis, Aplocheilus panchax, Apricaphanius saourensis, Archiaphyosemion guineense, Aristochromis christyi, Arius africanus, Arius festinus, Arius gigas, Arius latiscutatus, Arius madagascariensis, Arius uncinatus, Arnoglossus imperialis, Arnoldichthys spilopterus, Asprotilapia leptura, Xenotilapia leptura, Astatoreochromis alluaudi, Astatoreochromis straeleni, Astatoreochromis vanderhorsti, Astatotilapia bloyeti, Astatotilapia burtoni, Astatotilapia calliptera, Astatotilapia desfontainii, Astatotilapia paludinosa, Haplochromis paludinosus, Astatotilapia stappersii, Astatotilapia tweddlei, Atherina boyeri, Atherina caspia, Atherinomorus duodecimalis, Atopochilus chabanaudi, Atopochilus christyi, Atopochilus macrocephalus, Atopochilus mandevillei, Atopochilus pachychilus, Atopochilus savorgnani, Atopochilus vogti, Atopodontus adriaensi, Auchenoglanis biscutatus, Auchenoglanis occidentalis, Aulonocara aquilonium, Aulonocara auditor, Aulonocara baenschi, Aulonocara brevinidus, Aulonocara brevirostre, Aulonocara ethelwynnae, Aulonocara gertrudae, Aulonocara guentheri, Aulonocara hueseri, Aulonocara jacobfreibergi, Aulonocara kandeense, Aulonocara kandeensis, Aulonocara koningsi, Aulonocara korneliae, Aulonocara maylandi, Aulonocara nyassae, Aulonocara rostratum, Aulonocara saulosi, Aulonocara stonemani, Aulonocara stuartgranti, Aulonocara trematocephalum, Aulonocranus dewindti, Aurigequula fasciata, Auriglobus modestus, Austroglanis barnardi, Austroglanis gilli, Austroglanis sclateri, Awaous aeneofuscus, Awaous bustamantei, Awaous commersoni, Awaous lateristriga, Awaous macrorhynchus, Bagrus bajad, Bagrus caeruleus, Bagrus degeni, Bagrus docmak, Bagrus filamentosus, Bagrus lubosicus, Bagrus meridionalis, Bagrus orientalis, Bagrus ubangensis, Bagrus urostigma)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((54.9802 -21.6309,55.1382 -21.6954,55.1382 -20.4922,54.9305 -20.5721,54.7205 -21.0668,54.9802 -21.6309))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005570-250827131500795/datasets/export for details.
DOI: 10.34740/kaggle/dsv/12900329
title: Peer-to-Peer Boliviano (BOB) Exchange Data