cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/g175s-jz981
title: Vibrio cholerae SAD2112

description: SAD2112 (for T2SS only) = rpoS*, lacZ::lacIq, comEA-mCherry, ΔluxO, Ptac-tfoX, Ptac-recA, ∆TCP::ZeoR, ∆MSHA::CarbR, ∆CTX::KanR, ∆pilMNOPQ::TmR (aka ∆competence pilus) Ankur: "For the taxonomy ID - unfortunately the strain we sent does not have a taxonomy ID. So, you can use the generic one for V. cholerae which is "666". The strain we are working with is related to N16961, but is certainly not the same strain, so not sure if you would want to indicate that somehow? Just for reference - the strain we sent is E7946 (although it is obviously heavily modified with a number of mutations). "
description: <strong>Tilt Series Date:</strong> 2018-07-31</p>
<strong>Data Taken By:</strong> Sara Weaver</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> SAD2112</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, data collected by Sara Weaver</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Streaked stock on a plate. Grew up a single colony in 3 mL LB with shaking at 37˚C. The next day, subcultured 50uL of this overnight culture into 3mL of fresh LB+100uM IPTG + 20mM MgCl2 + 10mM CaCl2 and grow at 30˚C shaking for ~4 hours.  Note that the induction wasn't necessary for this delta T4 competence pili strain</p>
<strong>Sample Preparation:</strong> On 2018/07/12 spun gold (100 µL 10 nm gold + 25 µL 5% BSA) at 15,000rpm for 20 minutes, removed supernatant. Resuspended gold beads in 20 µL liquid culture. Vitrobot RT and 95% humidity, 3µL of gold/sample slurry on carbon/copper Quantifoil Finder grids R2/2 (EmiTech glow discharge 50 mA 120 s) Blot force +6, blot time 3 s, no waiting time, no drain time. Plunged into ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-07-31-31/rawdata/</p>2112I_tomogram30.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-07-31-31/rawdata/2112I_tomogram30.mrc"
        > <i class="download icon"></i> Download </a></p>

        2112I_tomogram30_full.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-07-31-31/3dimage_93893/2112I_tomogram30_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/03dky-83737
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/mka2019-10-25-8/rawdata/</p>Hpylori_FliO_008_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/mka2019-10-25-8/rawdata/Hpylori_FliO_008_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_008_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/mka2019-10-25-8/3dimage_107256/Hpylori_FliO_008_af_part40_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.c4p93c
title: Occurrence Download

description: A dataset containing 28408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Corvus splendens",
 "Country is United Arab Emirates",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28408 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006352-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jy8b3a
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Brienomyrus longianalis, Brycinus brevis, Brycinus carmesinus, Brycinus derhami, Brycinus grandisquamis, Brycinus leuciscus, Brycinus longipinnis, Brycinus luteus, Brycinus macrolepidotus, Brycinus poptae, Brycinus rhodopleura, Bryconaethiops boulengeri, Bryconaethiops macrops, Bryconaethiops microstoma, Bryconaethiops quinquesquamae, Bryconalestes derhami, Bryconalestes longipinnis, Bryconalestes tholloni, Buccochromis heterotaenia, Buccochromis lepturus, Buccochromis nototaenia, Buccochromis rhoadesii, Buccochromis spectabilis, Butis butis, Caecobarbus geertsii, Caffrogobius agulhensis, Callochromis macrops, Callochromis melanostigma, Callochromis pleurospilus, Callopanchax monroviae, Callopanchax occidentalis, Callopanchax toddi, Campylomormyrus alces, Campylomormyrus bredoi, Campylomormyrus cassaicus, Campylomormyrus christyi, Campylomormyrus curvirostris, Campylomormyrus elephas, Campylomormyrus luapulaensis, Campylomormyrus mirus, Campylomormyrus numenius, Campylomormyrus orycteropus, Campylomormyrus phantasticus, Campylomormyrus rhynchophorus, Campylomormyrus tamandua, Campylomormyrus tshokwe, Caprichromis liemi, Caprichromis orthognathus, Caranx sexfasciatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus moulouyensis, Carassius auratus, Carcharhinus leucas, Cardiopharynx schoutedeni, Carlarius latiscutatus, Carlarius parkii, Champsochromis caeruleus, Champsochromis spilorhynchus, Channa maculata, Channallabes alvarezi, Channallabes apus, Channallabes longicaudatus, Channallabes ogooensis, Channallabes sanghaensis, Channallabes teugelsi, Chanos chanos, Cheilochromis euchilus, Chelaethiops bibie, Chelaethiops congicus, Chelaethiops elongatus, Chelaethiops minutus, Chelaethiops rukwaensis, Chelidonichthys kumu, Chelon auratus, Chelon labrosus, Chelon melinopterus, Planiliza melinopterus, Chelon planiceps, Chelon ramada, Chelon saliens, Chelonodontops patoca, Chetia brevicauda, Chetia brevis, Chetia flaviventris, Chetia gracilis, Chetia mola, Chetia welwitschi, Chilochromis duponti, Chiloglanis angolensis, Chiloglanis anoterus, Chiloglanis asymetricaudalis, Chiloglanis batesii, Chiloglanis benuensis, Chiloglanis bifurcus, Chiloglanis brevibarbis, Chiloglanis camarabounyi, Chiloglanis cameronensis)",
 "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 ((5.9985 -1.8197,6.1596 -1.4443,5.9957 -1.0552,5.6304 -0.9035,5.2841 -1.0308,5.1008 -1.4539,5.2222 -1.7725,5.639 -1.9676,5.9985 -1.8197))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006353-250827131500795/datasets/export for details.
DOI: 10.22002/zsfyj-7hr16
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/mka2020-02-13-38/rawdata/</p>EPEC_8612_019_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/mka2020-02-13-38/rawdata/EPEC_8612_019_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_019_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/mka2020-02-13-38/3dimage_110893/EPEC_8612_019_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.wfurdu
title: Occurrence Download

description: A dataset containing 408444 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset includes 408444 records from 248 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006299-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ckbxk-wcw07
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/mka2019-11-19-63/rawdata/</p>Hpylori_dfliQ_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/mka2019-11-19-63/rawdata/Hpylori_dfliQ_078_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_078_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/mka2019-11-19-63/3dimage_108811/Hpylori_dfliQ_078_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dndaf-pf942
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/mka2019-11-19-211/rawdata/</p>Hpylori_dfliQ_212_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/mka2019-11-19-211/rawdata/Hpylori_dfliQ_212_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliQ_212_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/mka2019-11-19-211/3dimage_109083/Hpylori_dfliQ_212_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/wy65c-hgd40
title: Hpylori_dfliG

description: These are H. pylori cells that don't have a complete FliP. In addition, FliG 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 FliG 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/mka2019-11-23-47/rawdata/</p>Hpylori_dfliG_040_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/mka2019-11-23-47/rawdata/Hpylori_dfliG_040_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_dfliG_040_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/mka2019-11-23-47/3dimage_109405/Hpylori_dfliG_040_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/w0wkk-sdb35
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/mka2019-10-25-92/rawdata/</p>Hpylori_FliO_094_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Hpylori_FliO_094_af_part41_4.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>