cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/de07r-26a60
title: Caulobacter crescentus ftsE del

description: Caulobacter crescentus, ftsE, FtsZ, Long cell, PYE
description: <strong>Tilt Series Date:</strong> 2016-07-15</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: 200.0 eV/Å²,  defocus: -11.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFtomo</p>
<strong>Collaborators and Roles:</strong> Goley ED at Johns Hopkins University School of Medicine</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. Tilt Series Setting: single tilt. constant angular increment, step: 1.0. tilt range: (-60, 60).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-07-15-9/rawdata/</p>20007.mrc,  Tilt Series (Pixel Size 0.48 nm), 861.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-07-15-9/rawdata/20007.mrc"
        > <i class="download icon"></i> Download </a></p>

        20007.rec,  Reconstruction (Pixel Size 1.92 nm), 155.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2016-07-15-9/3dimage_76175/20007.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/110qd-18748
title: JV1644 Legionella thyA ΔdotO

description: JV1644 Legionella thyA ΔdotO. Lacks dotO ATPase.
description: <strong>Tilt Series Date:</strong> 2016-06-14</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: 1.5°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</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 at F30, Caltech.</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> 8 grids were frozen for the JV1644 strain at OD~2.9. 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/dga2016-06-14-71/rawdata/</p>DG_1644_150620163rd0041.mrc,  Tilt Series (Pixel Size 3.9 nm), 2.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        DG_1644_150620163rd0041.rec,  Reconstruction (Pixel Size 15.6 nm), 890.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dqa47-7nv41
title: JV3572

description: Legionella thyA ΔdotD
description: <strong>Tilt Series Date:</strong> 2016-04-02</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: 1.5°, 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 JV3572 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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-04-02-87/rawdata/</p>dg20160331_3572_atlas20047.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        dg20160331_3572_atlas20047_full.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.qd3yp2
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neoarius coatesi)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013586-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/91hma-8mv94
title: Agro_AD1484

description: Agro_AD1484 (AD1484:A348dB/pAD2079,virB on a multicopy plasmid).Cb resistance. Grown on induction plate pH5.8
description: <strong>Tilt Series Date:</strong> 2015-10-26</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 160.0 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</p>
<strong>Collaborators and Roles:</strong> Strain constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Agro_AD1484 (AD1484:A348dB/pAD2079,virB on a multicopy plasmid). Cells were scraped off the induction plate (particularly from the immediate surface of the plate: this is to ensure that if something is happening on the real surface of the plate, we do not miss it), dissolved in induction media, spun for 15 min in a table top centrifuge, supernatant thrown away, cells redissolved in PBS. Add gold to this: 1ul of gold to 4 ul of cells and freeze.</p>
<strong>Sample Preparation:</strong> 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.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-10-26-43/3dimage_70904/</p>20151026_AD1484_10011_full.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20151026_AD1484_10011.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/dga2015-10-26-43/rawdata/20151026_AD1484_10011.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/t1zaj-8g943
title: Agro_AD1408_from plate_20150831

description: Agro_AD1408_GFP-VirB11 (Kan+AS plates, Mes pH5.8). Add 400 ul of induction media to one of the induction plates (containing lawn of Agrobacterium AD1408) and wash the plate by gently rolling the liquid. I had 20ug/ml Kan to keep the cells happier. Add gold to this: 1ul of gold to 4 ul of cells and freeze.
description: <strong>Tilt Series Date:</strong> 2015-08-31</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1.0°, constant angular increment, dosage: 170.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> Strain constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline. This data was collected at the Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow AD1408 cells on AB solid medium (pH 7) at 30C. For induction, use one single colony and spread on induction plates (AB Mes pH 5.8) containing Kan (20ug/ml)+AS (200µM). Grow at 19C for 48 hr. Add 400 ul of induction media to one of the induction plates (containing lawn of Agrobacterium AD1408) and wash the plate by gently rolling the liquid. Add gold to this: 1ul of gold to 4 ul of cells, freeze.</p>
<strong>Sample Preparation:</strong> 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.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-08-31-55/3dimage_61126/</p>AD1408_plate_new10007_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        AD1408_plate_new10007.mrc,  Tilt Series (Pixel Size 0.48 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-08-31-55/rawdata/AD1408_plate_new10007.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ae28m-se610
title: JV1181

description: Legionella thyA ΔdotUF  (JV1181)
description: <strong>Tilt Series Date:</strong> 2017-02-02</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: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</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.</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> 4 grids were frozen. 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/dga2017-02-02-28/rawdata/</p>JV1181_02022017a0022.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        JV1181_02022017a0022_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8gwkb-fwf49
title: Ostreococcus tauri

description: Ostreococcus tauri, nitrogen
description: <strong>Tilt Series Date:</strong> 2006-11-26</p>
<strong>Data Taken By:</strong> Gregory Henderson</p>
<strong>Species / Specimen:</strong> Ostreococcus tauri</p>
<strong>Strain:</strong> RCC745</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 165.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod, bsoft</p>
<strong>Collaborators and Roles:</strong> prepared by Gregory Henderson and Lu Gan; cells provided by Herve Moreau</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in f/2 medium</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ghp2006-11-26-3/rawdata/</p>06nov26a_atlas4.mrc,  Tilt Series (Pixel Size 1.2 nm), 453.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.ffktrz
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum conjugatum",
 "Country is Dominican Republic",
 "HasCoordinate is true"
 ]
}

 The dataset includes 18 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013589-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p7f5yk
title: Occurrence Download

description: A dataset containing 4562 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Malus coronaria"
 ]
}

 The dataset includes 4562 records from 176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013587-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yjx589
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paspalum conjugatum",
 "Country is Micronesia (Federated States of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013590-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18167/dvn1/iiezks
title: Instrumental textural data for Boiled Cassava in Benin

description: This file contains instrumental textural data of boiled cassava that was collected by UAC-FSA team in Benin using a standard operating procedure.
DOI: 10.18167/dvn1/nodg6e
title: Food supply chains sustainability assessment of the mango sector in Burkina Faso

description: This dataset is joint with the scientific publication named "A Multiple food supply chains sustainability assessment of the mango sector in Burkina Faso" which details the challenges of the mango sub-sectors in Burkina Faso, the contribution of the Value Chain to economic growth and the analysis of its inclusiveness, the analysis of its social sustainability, and the analysis of its environmental sustainability.
DOI: 10.15468/dl.pzm8cs
title: Occurrence Download

description: A dataset containing 611 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Primula daonensis (Leyb.) Leyb."
 ]
}

 The dataset includes 611 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083592-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25526326
title: SNPs_all_matrix.FASTA

description: The SNP matrix file (SNPs_all_matrix.fasta) of 583 <i>S. aureus</i> isolates generated by kSNP3.021.
DOI: 10.5281/zenodo.10839521
title: ITSERR - dataset_1
DOI: 10.5281/zenodo.10839522
title: ITSERR - dataset_1
DOI: 10.5281/zenodo.10891876
title: ITSERR - dataset_1
DOI: 10.5281/zenodo.10908664
title: ITSERR - dataset_1
DOI: 10.5287/ora-b7ob4g8ba
title: Multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomic

description: Raw image file of scanned tissue sections acquired using Vectra Polaris imaging system. Scanned sections represent FFPE kidney sections from TLR7 agonist imiquimod treated mouse (IMQ) and matching controls (Ctrl), which are defined in the file labels
DOI: 10.15468/dl.jjhe8t
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calotriton arnoldi Carranza & Amat, 2005"
 ]
}

 The dataset's 1 records were derived from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083530-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10908358
title: GlioHyper: Glioma Biopsy Hyperspectral Dataset

description: A dataset of glioma biopsies which were examined using hyperspectral imaging. The details of the acquisition protocol and description of the data are provided in the accompaniying paper:

"A transportable hyperspectral imaging setup based on fast, high-density spectral scanning for in situ quantitative biochemical mapping of fresh tissue biopsies", Luca Giannoni et. al.
DOI: 10.5281/zenodo.10908359
title: GlioHyper: Glioma Biopsy Hyperspectral Dataset

description: A dataset of glioma biopsies which were examined using hyperspectral imaging. The details of the acquisition protocol and description of the data are provided in the accompaniying paper:

"A transportable hyperspectral imaging setup based on fast, high-density spectral scanning for in situ quantitative biochemical mapping of fresh tissue biopsies", Luca Giannoni et. al.
DOI: 10.5281/zenodo.10705895
title: Data for Ultrahigh Quality Factor of a Levitated Nanomechanical Oscillator

description: A levitated nanomechanical oscillator under ultra-high vacuum (UHV) is highly isolated fromits environment. It has been predicted that this isolation leads to very low mechanical dissipationrates. However, a gap persists between predictions and experimental data. Here, we levitate a silicananoparticle in a linear Paul trap at room temperature, at pressures as low as 7 × 10−11 mbar. Wemeasure a dissipation rate of 2π ×69(22) nHz, corresponding to a quality factor exceeding 1010, morethan two orders of magnitude higher than previously shown. A study of the pressure dependence ofthe particle’s damping and heating rates provides insight into the relevant dissipation mechanisms.
DOI: 10.5281/zenodo.7819825
title: Data for Ultrahigh Quality Factor of a Levitated Nanomechanical Oscillator

description: A levitated nanomechanical oscillator under ultra-high vacuum (UHV) is highly isolated fromits environment. It has been predicted that this isolation leads to very low mechanical dissipationrates. However, a gap persists between predictions and experimental data. Here, we levitate a silicananoparticle in a linear Paul trap at room temperature, at pressures as low as 7 × 10−11 mbar. Wemeasure a dissipation rate of 2π ×69(22) nHz, corresponding to a quality factor exceeding 1010, morethan two orders of magnitude higher than previously shown. A study of the pressure dependence ofthe particle’s damping and heating rates provides insight into the relevant dissipation mechanisms.
DOI: 10.15468/dl.rt5xxw
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calotriton arnoldi Carranza & Amat, 2005"
 ]
}

 The dataset's 1 records were derived from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083536-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.