cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/a3tnb-6cq56
title: COS7

description: Cos7 - not treatment, no transfection
description: <strong>Tilt Series Date:</strong> 2012-01-20</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Cells frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and plunge frozen</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-01-20-11/3dimage_69019/</p>12jan20_C106_2_COS7neg_AT1BT1_0018_part122_6.rec,  Reconstruction (Pixel Size 2.0 nm), 722.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-01-20-11/3dimage_69019/12jan20_C106_2_COS7neg_AT1BT1_0018_part122_6.rec"
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        12jan20_C106_2_COS7neg_AT1BT1_0018.mrc,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        12jan20_C106_2_COS7neg_AT1BT1_0018_part122_6.tiff,  file associated to 3D Image #69019, 1.6 MB  
        
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DOI: 10.5281/zenodo.16949978
title: Data release for the "Measurement of muon neutrino induced charged current interactions without charged pions in the final state using a new T2K off-axis near detector WAGASCI-BabyMIND"

description: Data release for "Measurement of muon neutrino induced charged current interactions without charged pions in the final state using a new T2K off-axis near detector WAGASCI-BabyMIND".

This folders contain the following files. Each file is explained as follows.



result_1d_momentum_dif.txt: contains one-dimensional differential cross section results as a function of momentum [CH,H2O]. The unit of the differential cross section and errors is 1e-39 [dsigma/dp].

result_1d_cosine_dif.txt: contains the values of the one-dimensional differential cross section results as a function of the cosine of muon momentum [CH,H2O]. The unit of the differential cross section and errors is 1e-39 [dsigma/dcos].

covariacne_matrix_momentum.txt: contains the values of the covariance matrix with the bins in the same order as in result_1d_diff_momentum.txt. The matrix is for the differential cross section as a function of muon momentum. The unit of each matrix element is 1e-78 [(dsigma/dp)^2].

covariacne_matrix_cosine.txt: contains the values of the covariance matrix with the bins in the same order as in result_1d_diff_cosine.txt. The matrix is for the differential cross section as a function of the cosine of muon angle. The unit of each matrix element is 1e-81 [(dsigma/dcos)^2].

flux_release.root: contains the flux covariance matrix and nominal flux for muon neutrino (numu), anti-muon neutrino (numub), electron neutrino (nue), and anti-electron neutrino (nueb).
DOI: 10.5281/zenodo.16949979
title: Data release for the "Measurement of muon neutrino induced charged current interactions without charged pions in the final state using a new T2K off-axis near detector WAGASCI-BabyMIND"

description: Data release for "Measurement of muon neutrino induced charged current interactions without charged pions in the final state using a new T2K off-axis near detector WAGASCI-BabyMIND".

This folders contain the following files. Each file is explained as follows.



result_1d_momentum_dif.txt: contains one-dimensional differential cross section results as a function of momentum [CH,H2O]. The unit of the differential cross section and errors is 1e-39 [dsigma/dp].

result_1d_cosine_dif.txt: contains the values of the one-dimensional differential cross section results as a function of the cosine of muon momentum [CH,H2O]. The unit of the differential cross section and errors is 1e-39 [dsigma/dcos].

covariacne_matrix_momentum.txt: contains the values of the covariance matrix with the bins in the same order as in result_1d_diff_momentum.txt. The matrix is for the differential cross section as a function of muon momentum. The unit of each matrix element is 1e-78 [(dsigma/dp)^2].

covariacne_matrix_cosine.txt: contains the values of the covariance matrix with the bins in the same order as in result_1d_diff_cosine.txt. The matrix is for the differential cross section as a function of the cosine of muon angle. The unit of each matrix element is 1e-81 [(dsigma/dcos)^2].

flux_release.root: contains the flux covariance matrix and nominal flux for muon neutrino (numu), anti-muon neutrino (numub), electron neutrino (nue), and anti-electron neutrino (nueb).
DOI: 10.22002/m7hah-pzt10
title: COS7 pNLGFP INF-alpha

description: Cos7 cells transfected with pNLGFP, treated with interferon-alpha 24 h post transfection and then frozen 24 h post interferon treatment. Sample #C110
description: <strong>Tilt Series Date:</strong> 2012-01-20</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> pNLGFP proviral construct provided by Irvin Chen UCLA. Sample prepared and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-01-20-42/3dimage_69082/</p>12jan20_C110_3_pNL_INFalpha_AT1BT10018_full.rec,  Reconstruction (Pixel Size 2.0 nm), 429.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-01-20-42/3dimage_69082/12jan20_C110_3_pNL_INFalpha_AT1BT10018_full.rec"
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        12jan20_C110_3_pNL_INFalpha_AT1BT10018.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        12jan20_C110_3_pNL_INFalpha_AT1BT10018_full.tiff,  file associated to 3D Image #69082, 866.8 kB  
        
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DOI: 10.15468/dl.mfgzu8
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pelasgus marathonicus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046654-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/dz0yn-6bs23
title: CLEM of TRIM5a-YFP in HeLa cells

description: HeLa cells expressing stable TRIM5a-YFP. Correlated light electron microscopy. Concentration of red 200 nm beads 1/300. 10 nm gold. Manual blotting. Cells grown on grids for 2 days and look vesiculated.
description: <strong>Tilt Series Date:</strong> 2014-06-17</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> Hela cells expressing TRIM5a-YFP</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 136.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD and Raptor</p>
<strong>Collaborators and Roles:</strong> Tom Hope and Wes Sundquist</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Gold London finder grids glow discharged twice. Concentration of red 200 nm beads 1/300 on grid. 10 nm gold. Manual blotting. Cells grown on grids for 2 days and look vesiculated.</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-06-17-3/rawdata/</p>tomography5.mrc,  Tilt Series (Pixel Size 0.6 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-06-17-3/rawdata/tomography5.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography5_full.rec,  Reconstruction (Pixel Size 2.4 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-06-17-3/3dimage_43974/tomography5_full.rec"
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        tomography5.rec,  Reconstruction (Pixel Size 0.0 nm), 421.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-06-17-3/3dimage_47847/tomography5.rec"
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DOI: 10.22002/0d6z0-b2t20
title: Myxococcus xanthus JK328

description: Bactofilin BacMNOP knockout strain.Imaged by Janelia Titan.Forgot to put in GIF slit during data collection...
description: <strong>Tilt Series Date:</strong> 2013-07-22</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Martin Thanbichler</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-07-22-10/rawdata/</p>07222013_Janelia_Myxo_JK328_0010.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-07-22-10/rawdata/07222013_Janelia_Myxo_JK328_0010.mrc"
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        07222013_Janelia_Myxo_JK328_0010_part131_41.rec,  Reconstruction (Pixel Size 1.68 nm), 430.6 MB  
        
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        07222013_Janelia_Myxo_JK328_0010_DB.rec,  Reconstruction (Pixel Size 0.0 nm), 258.4 MB  
        
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DOI: 10.22002/5wtt0-7a323
title: COS7 CHMP4A+VPS4DN

description: Cos7 cells transfected with CHMP4A & VPS4DN constructs
description: <strong>Tilt Series Date:</strong> 2012-01-06</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Constructs provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-01-06-27/3dimage_68901/</p>12jan06_c105_1_4ADNCos7_AT3BT10010_full.rec,  Reconstruction (Pixel Size 2.0 nm), 722.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-01-06-27/3dimage_68901/12jan06_c105_1_4ADNCos7_AT3BT10010_full.rec"
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        12jan06_c105_1_4ADNCos7_AT3BT10010.mrc,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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        12jan06_c105_1_4ADNCos7_AT3BT10010_full.tiff,  file associated to 3D Image #68901, 1.1 MB  
        
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DOI: 10.22002/d3hbf-6fk27
title: Calreticulin-YFP

description: Correlated light electron microscopy (CLEM) of calreticulin-YFP. The aim of the experiment was to determine whether ribosome associated granules contained calreticulin.
description: <strong>Tilt Series Date:</strong> 2014-10-21</p>
<strong>Data Taken By:</strong> Stephen Carter</p>
<strong>Species / Specimen:</strong> INS-1E Pancreatic Cells expressing Calreticulin-YFP</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Undefined</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Zach Freidberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> INS-1E cells grown on gold finder grids and plunge frozen using the vitrobot III blotted both sides pressure setting 1. Grids coated with fibronectin and 200 nm red fluorescent beads F8763 added to grids before freezing.</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-10-21-16/rawdata/</p>tomography7.mrc,  Tilt Series (Pixel Size 6.0 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-10-21-16/rawdata/tomography7.mrc"
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        tomography7_part121_1.rec,  Reconstruction (Pixel Size 24.0 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-10-21-16/3dimage_47342/tomography7_part121_1.rec"
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        tomography7_full.rec,  Reconstruction (Pixel Size 0.0 nm), 488.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scd2014-10-21-16/3dimage_48774/tomography7_full.rec"
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DOI: 10.22002/j8a6v-87d79
title: Myxococcus xanthus LL061

description: mCherry-bacP.First loaded in Titan cartridge and imaged in cryoLM.Imaged by UCLA Titan Krios.
description: <strong>Tilt Series Date:</strong> 2013-04-24</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 29100x. </p>
<strong>Acquisition Software:</strong> FEIbatchtomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Martin Thanbichler</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Au Finder 2/2.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-04-24-11/rawdata/</p>LL061_UCLA_correlated_20130424_13.mrc,  Tilt Series (Pixel Size 1.0 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-04-24-11/rawdata/LL061_UCLA_correlated_20130424_13.mrc"
        > <i class="download icon"></i> Download </a></p>

        LL061_UCLA_correlated_20130424_13_full.rec,  Reconstruction (Pixel Size 2.0 nm), 629.1 MB  
        
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        LL061_UCLA_correlated_20130424_13_bin2_DB.rec,  Reconstruction (Pixel Size 0.0 nm), 314.6 MB  
        
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DOI: 10.22002/bzk01-ag515
title: COS7 VPS4DN+CHMP4A

description: Cos7 cells co-transfected with VPS4DN and CHMP4A. Sample #C104
description: <strong>Tilt Series Date:</strong> 2012-02-04</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> Cercopithecus aethiops (monkey, African green)</p>
<strong>Strain:</strong> COS-7 ATCC CRL-1651</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> VPS4DN and CHMP4A constructs provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with lipofectamine</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-02-04-6/3dimage_68690/</p>12feb04_ATBT1_0006_full.rec,  Reconstruction (Pixel Size 2.0 nm), 722.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-02-04-6/3dimage_68690/12feb04_ATBT1_0006_full.rec"
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        12feb04_ATBT1_0006.mrc,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2012-02-04-6/rawdata/12feb04_ATBT1_0006.mrc"
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        12feb04_ATBT1_0006_full.tiff,  file associated to 3D Image #68690, 998.2 kB  
        
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