cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/8kn9n-3kk25
title: Pdj 122708 634

description: Prosthecobacter dejongeii, 09jan04b_pdj_624w1_034,
description: <strong>Tilt Series Date:</strong> 2009-01-04</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-01-04-20/rawdata/</p>09jan04b_pdj_624w1_034.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jan04b_pdj_624w1_034_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/5038g-emj57
title: Hyphomonas session9 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-03-07</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -8.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
  jsa2009-03-07-16_slicer9024.jpg: dividing cell, Hyphomonas neptunium
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-16/rawdata/</p>09mar07a_36c_016.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09mar07a_36c_016_full.rec,  Reconstruction (Pixel Size 1.264 nm), 419.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-16/3dimage_6901/09mar07a_36c_016_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.34740/kaggle/dsv/12872625
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.22002/gfjdb-6s311
title: VSVGpNL4GFP entry HUVECs

description: HUVECs 30 min post spinoculation with VSVGpNL4GFP
description: <strong>Tilt Series Date:</strong> 2011-08-12</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HUVECs</p>
<strong>Strain:</strong> </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> Proviral construct from Irvin Chen UCLA</p>
<strong>Purification / Growth Conditions / Treatment:</strong> infected VSVG pNL4GFP by spinoculation</p>
<strong>Sample Preparation:</strong> manual blot</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-08-12-28/rawdata/</p>11aug12_batch_0027.st,  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/cwl2011-08-12-28/rawdata/11aug12_batch_0027.st"
        > <i class="download icon"></i> Download </a></p>

        11aug12_batch_0027_full.rec,  Reconstruction (Pixel Size 2.0 nm), 528.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.15356014
title: Transcriptomic profiling of BrO, DMGO and GD2 CAR T cells: Processed datasets

description: Diffuse midline glioma (DMG) is a rare yet highly aggressive paediatric cancer primarily arising in the pontine region of the brainstem, necessitating the development of patient-representative models for treatment advance. Here, we developed an FGF4-driven human brainstem organoid model. By genetically engineering de novo H3.3K27M-altered DMG, we demonstrate that brainstem-pontine glial specification is critical for DMG tumorigenesis, yielding infiltrative tumors that recapitulate patient-specific molecular heterogeneity. Prolonged GD2 CAR T cell treatment mirrors clinical outcome variability, reveals extensive transcriptional heterogeneity, and enables identification of both potent effector and dysfunctional populations. Furthermore, incorporation of brain-resident myeloid cells generated DMG-specific microglia that reduced GD2 CAR T cell efficacy and revealed the functional states most vulnerable to microglia-mediated immune suppression. Thus, we present a novel human DMG model offering a months-long experimental window in vitro, which we leverage to delineate CAR T cell functionality and microglial impact, aiding therapy development for this devastating disease.
description: Describtion of the datasets:

bro_timecourse_cleaned.h5ad

Non-perturbed neural cells captured at eight different timepoints during the BrO differentiation protocol. Allows detailed analysis of BrO development and comparison with human counterparts.

dmgo_cleaned.h5ad

DMG tumor cells isolated from DMGO organoids, enriched using FACS. Designed to investigate the different tumor states and enables comparison with the BrO timecourse and DMG patients. 

T_Cells_BRO_n1_processed:GD2 CAR T cells isolated from DMGO organoids after co-culture, from experiment n1. Captures the post-exposure transcriptional response of CAR T cells.

T_Cells_BRO_n3_processed:Combined dataset from three experiments including different conditions: GD2 CAR T cells unexposed to DMGO, exposed to DMGO, and sorted populations (NCAM1+ and NCAM1–) after exposure. Enables comparison across activation and phenotypic states.

Sortseq_CAR:Sort-seq experiment of GD2 CAR T cells under various conditions: unexposed, exposed to DMGO, and co-cultured with or without microglia. Designed to dissect CAR T cell responses in different microenvironments.

Sortseq_MG:Sort-seq dataset of PMPs (microglia-like cells) exposed to different organoid contexts: unexposed, co-cultured with pontine organoids, or with DMGO. Aims to profile microglial activation under tumor and non-tumor conditions.
DOI: 10.15468/dl.bec24j
title: Occurrence Download

description: A dataset containing 4331 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Chinese Taipei)",
 "TaxonKey is Pyracantha fortuneana"
 ]
}

 The dataset includes 4331 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045732-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qnbbwe
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Manta alfredi"
 ]
}

 The dataset includes 106 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045733-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/s3qpz-3s417
title: Eco 120208 012

description: Escherichia coli, 09feb08c_6_1_2_120208_012_070,
description: <strong>Tilt Series Date:</strong> 2009-02-08</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 6.1.2 Martin</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-02-08-20/rawdata/</p>09feb08c_6_1_2_120208_012_070.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09feb08c_6_1_2_120208_012_070_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9me72-a7c33
title: Hyphomicrobium facile session13 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-04-14</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomicrobium facile</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1.5°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in ATCC-656 media...</p>
<strong>Sample Preparation:</strong> C-flat grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-14-21/rawdata/</p>09apr14a_Bhf2b_022.mrc,  Tilt Series (Pixel Size 0.632 nm), 738.2 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09apr14a_Bhf2b_022_full.rec,  Reconstruction (Pixel Size 1.264 nm), 314.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8nrrc-85d29
title: MamJ deletion (and might contain

description: Raw data files of MamJ deletion (and might contain
description: <strong>Tilt Series Date:</strong> 2010-02-18</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Magnetospirillum magneticum</p>
<strong>Strain:</strong> AMB-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1.5°, constant angular increment, dosage: 110.0 eV/Å²,  defocus: -15.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR and Peach</p>
<strong>Collaborators and Roles:</strong> Cell culture were from Arash Komeili. Upon receiving, cells were frozen in 2 hours. Meanwhile they were kept in 30C. Data collected and processed by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Stationary phase. </p>
<strong>Sample Preparation:</strong> R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-02-18-3/rawdata/</p>10feb18a_dJnofe2_003.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe2_003_full.rec,  Reconstruction (Pixel Size 2.384 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xpwmm-9k945
title: Eco 031910 MP49

description: Escherichia coli, 10mar24a_MP_49_021,
description: <strong>Tilt Series Date:</strong> 2010-03-24</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 19.1 Martin</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-03-24-12/rawdata/</p>10mar24a_MP_49_021.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        10mar24a_MP_49_021.rec,  Reconstruction (Pixel Size 1.9 nm), 396.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/pz82t-wrf46
title: Hyphomonas session20 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-07-13</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in 2216 media, filtered flowthrough grow long time at 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-13-1/rawdata/</p>09jul13a_b624a_001.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul13a_b624a_001_full.rec,  Reconstruction (Pixel Size 1.264 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/jqprp-mng13
title: Hyphomonas EB session21 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-07-14</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, EB 0.02mg/ml overnight 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
  jsa2009-07-14-101_slicer8941.jpg: Hyphomonas neptunium .  unknown filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-07-14-101/rawdata/</p>09jul14a_b200c_102.mrc,  Tilt Series (Pixel Size 0.632 nm), 511.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul14a_b200c_102_part.rec,  Reconstruction (Pixel Size 1.264 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/59t04-4s770
title: Pdj 121509 MP34

description: Prosthecobacter dejongeii, 09dec18a_MP34_Pdj_047, putative btub structure (2 tubes),
description: <strong>Tilt Series Date:</strong> 2009-12-18</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
  mpa2009-12-18-44_slicer4397.jpg: Vesicles mpa2009-12-18-44_slicer4398.jpg: Pilli mpa2009-12-18-44_slicer4400.jpg: Filaments mpa2009-12-18-44_slicer4401.jpg: Unknown
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-12-18-44/rawdata/</p>09dec18a_MP34_Pdj_047.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09dec18a_MP34_Pdj_047_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.s6zv3w
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriobotrya japonica",
 "Country is Trinidad and Tobago",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045734-250811113504898/datasets/export for details.
DOI: 10.15468/dl.erb7gp
title: Occurrence Download

description: A dataset containing 4221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eriobotrya japonica",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4221 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045735-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/hn4wa-1kh95
title: Pdj 121509 MP34

description: Prosthecobacter dejongeii, 09dec18a_MP34_Pdj_058,
description: <strong>Tilt Series Date:</strong> 2009-12-18</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter dejongeii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-12-18-52/rawdata/</p>09dec18a_MP34_Pdj_058.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        09dec18a_MP34_Pdj_058_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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