cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/n0dcq-mh224
title: Lp02_2nd

description: 2nd time collection: Jan 2016. Defocus -6.Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0
description: <strong>Tilt Series Date:</strong> 2016-01-15</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> Grids were stored in Janelia from previous imaging. See previous Lp02 sample prep. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-6/3dimage_72789/</p>tomo_area1000100010004_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-6/3dimage_72789/tomo_area1000100010004_full.rec"
        > <i class="download icon"></i> Download </a></p>

        tomo_area1000100010004.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-6/rawdata/tomo_area1000100010004.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16992348
title: GTnum Pléiades questionnaire

description: Questionnaire sur la classe virtuelle pendant le confinement diffusé dans le cadre de la recherche GTnum Pléiades financée par la Direction du numérique éducatif (Ministère de l'Education Nationale, France) pilotée par le laboratoire Circeft.
DOI: 10.5281/zenodo.7230389
title: GTnum Pléiades questionnaire

description: Questionnaire sur la classe virtuelle pendant le confinement diffusé dans le cadre de la recherche GTnum Pléiades financée par la Direction du numérique éducatif (Ministère de l'Education Nationale, France) pilotée par le laboratoire Circeft.
DOI: 10.22002/ayz7r-4k707
title: JV7058

description: JV7058 is a triple deletion that lacks dotH (distant VirB9 homolog), dotG (distant VirB10 homolog) and dotF. Lp02.
description: <strong>Tilt Series Date:</strong> 2016-03-31</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV7058 strain (2x and 3x concentrated from OD-3 culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
  dga2016-03-31-76_slicer16860.jpg: Chain of vesicles
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-03-31-76/rawdata/</p>dg20160330_7058_atlas70031.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        dg20160330_7058_atlas70031_part81_2.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.uvj7tz
title: Occurrence Download

description: A dataset containing 235 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macropodium nivale"
 ]
}

 The dataset includes 235 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006581-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uttsd5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chiloglanis carnosus, Chiloglanis congicus, Chiloglanis deckenii, Chiloglanis devosi, Chiloglanis dialloi, Chiloglanis disneyi, Chiloglanis elisabethianus, Chiloglanis emarginatus, Chiloglanis fasciatus, Chiloglanis harbinger, Chiloglanis kabaensis, Chiloglanis kalambo, Chiloglanis kerioensis, Chiloglanis kolente, Chiloglanis lamottei, Chiloglanis loffabrevum, Chiloglanis longibarbis, Chiloglanis lufirae, Chiloglanis lukugae, Chiloglanis macropterus, Chiloglanis marlieri, Chiloglanis mbozi, Chiloglanis microps, Chiloglanis modjensis, Chiloglanis mongoensis, Chiloglanis neumanni, Chiloglanis niger, Chiloglanis niloticus, Chiloglanis normani, Chiloglanis nzerekore, Chiloglanis occidentalis, Chiloglanis paratus, Chiloglanis pezoldi, Chiloglanis pojeri, Chiloglanis polyodon, Chiloglanis polypogon, Chiloglanis pretoriae, Chiloglanis reticulatus, Chiloglanis rukwaensis, Chiloglanis ruziziensis, Chiloglanis sanagaensis, Chiloglanis sardinhai, Chiloglanis somereni, Chiloglanis swierstrai, Chiloglanis trilobatus, Chiloglanis tweddlei, Chiloglanis voltae, Chiloglanis waterloti, Chilotilapia euchilus, Chilotilapia rhoadesii, Chindongo ater, Chindongo bellicosus, Chindongo cyaneus, Chindongo demasoni, Chindongo flavus, Chindongo heteropictus, Maylandia heteropicta, Chindongo longior, Chindongo minutus, Chindongo saulosi, Chromidotilapia cavalliensis, Chromidotilapia elongata, Chromidotilapia guntheri, Chromidotilapia kingsleyae, Chromidotilapia linkei, Chromidotilapia mamonekenei, Chromidotilapia melaniae, Chromidotilapia mrac, Chromidotilapia nana, Chromidotilapia regani, Chromidotilapia schoutedeni, Chrysichthys aluuensis, Chrysichthys ansorgii, Chrysichthys auratus, Chrysichthys bocagii, Chrysichthys brachynema, Chrysichthys brevibarbis, Chrysichthys cranchii, Chrysichthys dageti, Chrysichthys delhezi, Chrysichthys dendrophorus, Chrysichthys duttoni, Chrysichthys furcatus, Chrysichthys nigrodigitatus, Chrysichthys grandis, Chrysichthys graueri, Chrysichthys habereri, Chrysichthys helicophagus, Chrysichthys hildae, Chrysichthys johnelsi, Chrysichthys laticeps, Chrysichthys levequei, Chrysichthys longibarbis, Chrysichthys longidorsalis, Chrysichthys longipinnis, Chrysichthys mabusi, Chrysichthys macropterus, Chrysichthys maurus, Chrysichthys nyongensis)",
 "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 ((45.0245 -12.136,44.6652 -11.6088,43.9782 -11.7142,43.8575 -11.1854,43.5561 -10.9013,42.9255 -11.043,42.7331 -11.7654,43.2052 -12.6542,43.4803 -12.8847,44.5705 -12.8806,44.7256 -13.3177,45.1376 -13.5063,45.5464 -13.3432,45.7456 -13.0171,45.7852 -12.6623,45.638 -12.4031,45.0245 -12.136))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006582-250827131500795/datasets/export for details.
DOI: 10.22002/b3k1y-pc559
title: Lp02_2nd

description: 2nd time collection: Jan 2016. Defocus -6.Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0
description: <strong>Tilt Series Date:</strong> 2016-01-15</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> Grids were stored in Janelia from previous imaging. See previous Lp02 sample prep. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-20/3dimage_72825/</p>tomo_area1000100010010_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-20/3dimage_72825/tomo_area1000100010010_full.rec"
        > <i class="download icon"></i> Download </a></p>

        tomo_area1000100010010.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-01-15-20/rawdata/tomo_area1000100010010.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16962780
title: Global Observation-based LInear Vorticity Vertical Velocities (OLIV3) over isopycnal levels

description: Observation-based Linear Vorticity Vertical Velocities (OLIV3) estimates from observation-based geostrophic velocities within the global themocline during the 1993-2019 period at annual frequency.

The beta-plane geostrophic OLIV3 fields are computed following the Indefinite depth-integrated geostrophic linear vorticity balance methodology described in Cortés-Morales and Lazar, 2024, Diego Cortés Morales, 2023 [thesis] and Cortés-Morales et al., (submitted) applied to the ARMOR3D [Mulet et al., 2013; https://data.marine.copernicus.eu/product/MULTIOBS_GLO_PHY_TSUV_3D_MYNRT_015_012] geostrophic meridional velocities. The boundary condition used is the Ekman pumping vertical velocities computed from ERA5 wind stress [DOI: 10.24381/cds.f17050d7]. The velocity field is quality-flagged based on the relative error and interannual correlation coefficient between w_g and w_tot in an OGCM perfect model test (Cortés-Morales et al., (submitted)).

----------------------------------------------------------------------------------------

Geographical coverage: Global Ocean

Grid and horizontal spatial resolution: Evenly spaced 0.25º grid

Vertical levels: 71 levels from sigma level 21 to 28.17 kg/m^3.

Temporal resolution: Annual (1993-2019)

-----------------------------------------------------------------------------------------

Variables:

lon (2D): Longitude

lat (2D): Latitude

isolev (1D): Isopycnal level

time (1D): Year

w_oliv3(4D): Beta-plane geostrophic vertical velocities

h_depth (4D): Depth isopycnal surfaces

flag_time_var (3D): Flag based on correlation coeffcient between geostrophic and total vertical velocties from OGCM

flag_time_mean (3D): flag based on relative error between geostrophic and total vertical velocties from OGCM
DOI: 10.5281/zenodo.7857245
title: Global Observation-based LInear Vorticity Vertical Velocities (OLIV3) over isopycnal levels

description: Observation-based Linear Vorticity Vertical Velocities (OLIV3) estimates from observation-based geostrophic velocities within the global themocline during the 1993-2019 period at annual frequency.

The beta-plane geostrophic OLIV3 fields are computed following the Indefinite depth-integrated geostrophic linear vorticity balance methodology described in Cortés-Morales and Lazar, 2024, Diego Cortés Morales, 2023 [thesis] and Cortés-Morales et al., (submitted) applied to the ARMOR3D [Mulet et al., 2013; https://data.marine.copernicus.eu/product/MULTIOBS_GLO_PHY_TSUV_3D_MYNRT_015_012] geostrophic meridional velocities. The boundary condition used is the Ekman pumping vertical velocities computed from ERA5 wind stress [DOI: 10.24381/cds.f17050d7]. The velocity field is quality-flagged based on the relative error and interannual correlation coefficient between w_g and w_tot in an OGCM perfect model test (Cortés-Morales et al., (submitted)).

----------------------------------------------------------------------------------------

Geographical coverage: Global Ocean

Grid and horizontal spatial resolution: Evenly spaced 0.25º grid

Vertical levels: 71 levels from sigma level 21 to 28.17 kg/m^3.

Temporal resolution: Annual (1993-2019)

-----------------------------------------------------------------------------------------

Variables:

lon (2D): Longitude

lat (2D): Latitude

isolev (1D): Isopycnal level

time (1D): Year

w_oliv3(4D): Beta-plane geostrophic vertical velocities

h_depth (4D): Depth isopycnal surfaces

flag_time_var (3D): Flag based on correlation coeffcient between geostrophic and total vertical velocties from OGCM

flag_time_mean (3D): flag based on relative error between geostrophic and total vertical velocties from OGCM
DOI: 10.22002/2ppvg-dv782
title: FtsZ arc on one side

description: FtsZ arc on the invagination side (left)FstZ arc looks incomplete, vanishing before the missing wedge (green arrow).
description: <strong>Tilt Series Date:</strong> 2015-03-10</p>
<strong>Data Taken By:</strong> Qing Yao</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> C. crescentus was from Yi-Wei's cryo-stock and was grown in PYE medium overnight at 30°c 250 rpm. In the next days' morning, 1/20 subculture into the M2G medium. When OD600 reaches 0.30, 2 ml medium was spun down gently (3000 rpm for 3 min) and the resuspension was 100 ul for cryo-grid preparation.</p>
<strong>Sample Preparation:</strong> Glow discharged Quantifoil R2/R holey carbon film. 4 ul concentrated gold suspension was added to 16 ul bacteria and mix before plunge freezing. Plunge freezing condition: 6(force)-2(duration time)-1(dry time). Tilt Series Setting: single tilt. constant angular increment, step: 1. tilt range: (-60, 60). dosage: 180/A2. defocus: -10 um. magnification: 27500.</p>
  qya2015-03-10-20_slicer12823.jpg: Other kind of filaments bundle with clear pattern. qya2015-03-10-20_slicer12824.jpg: Invagination maybe on one side qya2015-03-10-20_slicer12825.jpg: FtsZ arc on the invagination side (Left). The arc appears incomplete and ends before the missing wedge (green arrow) qya2015-03-10-20_slicer13015.jpg: FtsZ from invagination side
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2015-03-10-20/rawdata/</p>Qing15_10020.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2015-03-10-20/rawdata/Qing15_10020.mrc"
        > <i class="download icon"></i> Download </a></p>

        Qing15_10020_part121_8.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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DOI: 10.22002/7hvzx-1ba23
title: Lp02_Legionella pneumophila

description: Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in  AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0
description: <strong>Tilt Series Date:</strong> 2015-10-29</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor, also manually processed 25 tomograms (and used SIRT)for subtomogram averaging.</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lp02 is thymidine auxotroph of the parental strain Lp01 originating from Philadelphia-1 strain. Cells were grown in  AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0. Added gold before freezing.</p>
<strong>Sample Preparation:</strong> 4 grids were frozen for Lp02 at OD= 2.8 and another 4 grids for Lp02 at OD= 3.3Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-29-50/3dimage_70737/</p>20151029_LP02_10021_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20151029_LP02_10021.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.3 GB  
        
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