cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/w5ctz-asb80
title: lip9-3 (+ megacomplex)

description: Exposure 1s
description: <strong>Tilt Series Date:</strong> 2020-10-05</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: 88.0 eV/Å²,  defocus: -10.0 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/wnj2020-10-05-16/rawdata/</p>lip9-3-sq1-tg7.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/wnj2020-10-05-16/rawdata/lip9-3-sq1-tg7.mrc"
        > <i class="download icon"></i> Download </a></p>

        lip9-3-sq1-tg7_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/wnj2020-10-05-16/3dimage_115837/lip9-3-sq1-tg7_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/226-fjf-al9
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/46m-ny0-hf4
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6e2-6cc-cac
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ce1-jh9-32g
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g00-yaa-tkj
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zzx-4pl-78c
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c2b-dl9-t8h
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/vtwhn-ttw88
title: Vibrio cholerae SAD2095 induced

description: SAD2095 (T2SS and T4 competence pili) = rpoS*, pilA S81C, lacZ::lacIq, comEA-mCherry, ΔluxO, Ptac-tfoX, Ptac-recA, ∆TCP::ZeoR, ∆MSHA::CarbR, ∆CTX::KanR, ∆pilT::TmRAnkur: "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> 2018-08-13</p>
<strong>Data Taken By:</strong> Sara Weaver</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> SAD2095</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 0.0 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 416 uL of this overnight culture into 25 mL of fresh LB+100uM IPTG + 20mM MgCl2 + 10mM CaCl2 in a 125 mL beveled glass flask and grow at 30˚C shaking for ~6 hours.</p>
<strong>Sample Preparation:</strong> Grid SW0808A2 - 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, vortex sample immediately before taking 4 µL of gold/sample slurry on carbon/copper Quantifoil Finder grids R2/2 (EmiTech glow discharge 20 mA, 60 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/swj2018-08-13-43/rawdata/</p>0808A2_tomo35.mrc,  Tilt Series (Pixel Size 0.39 nm), 710.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-08-13-43/rawdata/0808A2_tomo35.mrc"
        > <i class="download icon"></i> Download </a></p>

        0808A2_tomo35_part25_1.rec,  Reconstruction (Pixel Size 1.56 nm), 711.2 MB  
        
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DOI: 10.22002/0wte0-rfd11
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/mka2019-11-24-86/rawdata/</p>Hpylori_dfliM_089_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
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        Hpylori_dfliM_089_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: 10.3535/f9c-ae3-kfj
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xwf-8f1-0xd
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0ga-kry-dw3
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wtn-r7n-hp8
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xr4-gxq-4zh
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/12z-j72-q70
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m9z-cw2-4mb
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bes-syz-qz2
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.22002/8gb5b-59196
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/mka2019-10-28-112/rawdata/</p>Hpylori_FliM_114_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_FliM_114_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: 10.15468/dl.de4bjg
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chloris barbata",
 "Country is Peru",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012110-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmrvk6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chloris barbata",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012112-250827131500795/datasets/export for details.
DOI: 10.15468/dl.dj6vk2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chloris barbata",
 "Country is Qatar",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012111-250827131500795/datasets/export for details.
DOI: 10.22002/h9pb2-yk207
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/mka2019-09-21-15/rawdata/</p>Hpylori_dFliO8_good.mrc,  Tilt Series (Pixel Size 0.4494 nm), 2.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        Hpylori_dFliO8_good_full.rec,  Reconstruction (Pixel Size 1.7976 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.3535/nhp-0tb-hmb
title: Coleoidea Bather, 1888

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/aft-cbr-wfr
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vr7-z2d-bar
title: Mollusca

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z0h-geb-xyw
title: Coleoidea Bather, 1888

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7pq-wn1-r42
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e7k-xa2-6lp
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rjs-tpp-77q
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ja2-nvb-j6f
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jkv-e9r-er1
title: †Ammonoidea

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lkq-vpm-2tk
title: Coleoidea Bather, 1888

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.wez9ma
title: Occurrence Download

description: A dataset containing 1601 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydrocharis dubia"
 ]
}

 The dataset includes 1601 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012109-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh3425283.08fu
title: SH3425283.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3425284.08fu
title: SH3425284.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3425285.08fu
title: SH3425285.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3425286.08fu
title: SH3425286.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3425287.08fu
title: SH3425287.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.