cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/8s1gg-5av13
title: Pva 020710 MP47

description: Prosthecobacter vanneervenii, 10feb07a_MP47_Pva_exp_078, putative btub structure (2 tubes),
description: <strong>Tilt Series Date:</strong> 2010-02-07</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter vanneervenii</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: -8.0 μm,  magnification: 27500x. </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>
  mpa2010-02-07-68_slicer9281.jpg: filament, Prosthecobacter vanneervenii
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-02-07-68/rawdata/</p>10feb07a_MP47_Pva_exp_078.mrc,  Tilt Series (Pixel Size 0.95 nm), 914.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-02-07-68/rawdata/10feb07a_MP47_Pva_exp_078.mrc"
        > <i class="download icon"></i> Download </a></p>

        10feb07a_MP47_Pva_exp_078_part.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2010-02-07-68/3dimage_14645/10feb07a_MP47_Pva_exp_078_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.7tbc7z
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ianthocincla bieti",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045687-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/h427t-8pt07
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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-31/rawdata/</p>09mar07a_36c_032.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-03-07-31/rawdata/09mar07a_36c_032.mrc"
        > <i class="download icon"></i> Download </a></p>

        09mar07a_36c_032_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/jsa2009-03-07-31/3dimage_6930/09mar07a_36c_032_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/66rgf-32757
title: HIV gag session12 41KX

description: Opti-prep HIV gag shell
description: <strong>Tilt Series Date:</strong> 2009-04-13</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> HIV cores</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 2°, constant angular increment, dosage: 72.0 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 Virgine; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Opti-prep</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/jsa2009-04-13-8/rawdata/</p>09apr13a_b19a_008.mrc,  Tilt Series (Pixel Size 0.512 nm), 570.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-13-8/rawdata/09apr13a_b19a_008.mrc"
        > <i class="download icon"></i> Download </a></p>

        09apr13a_b19a_008_full.rec,  Reconstruction (Pixel Size 1.024 nm), 293.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-13-8/3dimage_7473/09apr13a_b19a_008_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/azvn9-y8q80
title: Calubactor EB session22 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-08-07</p>
<strong>Data Taken By:</strong> Jian Shi</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°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 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 Zhuo/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>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-08-07-33/rawdata/</p>09aug07a_b266c_043.mrc,  Tilt Series (Pixel Size 0.774 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-08-07-33/rawdata/09aug07a_b266c_043.mrc"
        > <i class="download icon"></i> Download </a></p>

        09aug07a_b266c_043_part.rec,  Reconstruction (Pixel Size 1.548 nm), 419.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-08-07-33/3dimage_8456/09aug07a_b266c_043_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/g0jcv-9at62
title: Pfl 121509 MP26

description: Prosthecobacter fluviatilis, 09dec18a_MP26___Pfl_020,
description: <strong>Tilt Series Date:</strong> 2009-12-18</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter fluviatilis</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>
  mpa2009-12-18-18_slicer9383.jpg: Prosthecobacter fluviatilis  .  filament mpa2009-12-18-18_slicer9385.jpg: Prosthecobacter fluviatilis  .  filament
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-12-18-18/rawdata/</p>09dec18a_MP26___Pfl_020.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-12-18-18/rawdata/09dec18a_MP26___Pfl_020.mrc"
        > <i class="download icon"></i> Download </a></p>

        09dec18a_MP26___Pfl_020_part.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-12-18-18/3dimage_14271/09dec18a_MP26___Pfl_020_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/pnvxr-ke691
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/zla2010-02-18-8/rawdata/</p>10feb18a_dJnofe2_008.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2010-02-18-8/rawdata/10feb18a_dJnofe2_008.mrc"
        > <i class="download icon"></i> Download </a></p>

        10feb18a_dJnofe2_008_full.rec,  Reconstruction (Pixel Size 2.384 nm), 524.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16947474
title: Code and associated data directory for manuscript: Spatially Resolved Microglial Expression Around Aβ Plaques in Human Alzheimer's Disease Tissue

description: Code and accompanying data directory for the manuscript below. Data have been pre-processed through the following steps: FASTQ → DCC → probe-level quality control. The raw FASTQ and DCC files are available from NCBI GEO.

Title

Spatially Resolved Microglial Expression Around Aβ Plaques in Human Alzheimer’s Disease Tissue

 

Authors

Jack I. Wood1,2, Georgia Ppasia1,3#, Paul Rolland-Du-Roscoat1,4#, Sneha Desai1,2, Shamim Choudhury1, Aya Balbaa1, Daria Gavriouchkina5, Modesta Blunskyte5, John Hardy5,6, Damian M. Cummings1, Dervis Salih5, Jörg Hanrieder2,6, Frances A. Edwards1*

 

Affiliations

1 Department of Neuroscience, Physiology & Pharmacology, University College London, Gower Street, London WC1E 6BT, U

2 Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, House V3, 43180 Mölndal, Sweden

3 Sainsbury Wellcome Centre, UCL, London, W1T 4JG, UK

4 Ecole Normale Supérieure Paris-Saclay, 91190 Gif-sur-Yvette, France

5 UK Dementia Research Institute, University College London, Gower Street, London WC1E 6BT, UK 

6 Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK

 

Experimental summary

NanoString GeoMx Digital Spatial Profiler (DSP) was applied to FFPE human hippocampus to profile microglia-enriched gene expression from donors with Alzheimer’s disease (AD) and cognitively unimpaired, amyloid-positive (CU-AP) controls. For each tissue, gene expression was captured from microglia directly contacting amyloid plaques (“plaque-associated”), (ii) microglia in the peri-plaque region, and (iii) microglia distant from plaques.

 

Manuscript Abstract

Using microglia-enriched spatial transcriptomics on human Alzheimer’s disease tissue, we identify distinct gene expression changes across microglia located in direct contact with plaques, in periplaque regions, and in areas distant from plaques. We define a group of plaque contact–only microglial (PCOM) genes whose expression increases exclusively in microglia directly contacting plaques. These genes show significant overlap with previously reported gene sets, suggesting that plaque-contacting microglia correspond to the well-characterised disease-associated microglia (DAM) and other AD-related gene-expression signatures. We further identify distinct co-expression networks associated with disease-relevant covariates, including an immune module linked to APOE genotype and a synaptic–mitochondrial module negatively associated with Braak stage. Finally, we compare the human dataset to our previously published data from 18-month-old AppNL-F mice, generated using the same experimental paradigm and demonstrate cross-species concordance in gene expression within plaque-contacting microglia.
DOI: 10.5281/zenodo.16947475
title: Code and associated data directory for manuscript: Spatially Resolved Microglial Expression Around Aβ Plaques in Human Alzheimer's Disease Tissue

description: Code and accompanying data directory for the manuscript below. Data have been pre-processed through the following steps: FASTQ → DCC → probe-level quality control. The raw FASTQ and DCC files are available from NCBI GEO.

Title

Spatially Resolved Microglial Expression Around Aβ Plaques in Human Alzheimer’s Disease Tissue

 

Authors

Jack I. Wood1,2, Georgia Ppasia1,3#, Paul Rolland-Du-Roscoat1,4#, Sneha Desai1,2, Shamim Choudhury1, Aya Balbaa1, Daria Gavriouchkina5, Modesta Blunskyte5, John Hardy5,6, Damian M. Cummings1, Dervis Salih5, Jörg Hanrieder2,6, Frances A. Edwards1*

 

Affiliations

1 Department of Neuroscience, Physiology & Pharmacology, University College London, Gower Street, London WC1E 6BT, U

2 Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, House V3, 43180 Mölndal, Sweden

3 Sainsbury Wellcome Centre, UCL, London, W1T 4JG, UK

4 Ecole Normale Supérieure Paris-Saclay, 91190 Gif-sur-Yvette, France

5 UK Dementia Research Institute, University College London, Gower Street, London WC1E 6BT, UK 

6 Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK

 

Experimental summary

NanoString GeoMx Digital Spatial Profiler (DSP) was applied to FFPE human hippocampus to profile microglia-enriched gene expression from donors with Alzheimer’s disease (AD) and cognitively unimpaired, amyloid-positive (CU-AP) controls. For each tissue, gene expression was captured from microglia directly contacting amyloid plaques (“plaque-associated”), (ii) microglia in the peri-plaque region, and (iii) microglia distant from plaques.

 

Manuscript Abstract

Using microglia-enriched spatial transcriptomics on human Alzheimer’s disease tissue, we identify distinct gene expression changes across microglia located in direct contact with plaques, in periplaque regions, and in areas distant from plaques. We define a group of plaque contact–only microglial (PCOM) genes whose expression increases exclusively in microglia directly contacting plaques. These genes show significant overlap with previously reported gene sets, suggesting that plaque-contacting microglia correspond to the well-characterised disease-associated microglia (DAM) and other AD-related gene-expression signatures. We further identify distinct co-expression networks associated with disease-relevant covariates, including an immune module linked to APOE genotype and a synaptic–mitochondrial module negatively associated with Braak stage. Finally, we compare the human dataset to our previously published data from 18-month-old AppNL-F mice, generated using the same experimental paradigm and demonstrate cross-species concordance in gene expression within plaque-contacting microglia.
DOI: 10.15468/dl.9nrkta
title: Occurrence Download

description: A dataset containing 1022 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Pyracantha atalantioides"
 ]
}

 The dataset includes 1022 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045688-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/k4etb-s1c43
title: BsubtilisMJ007

description: Bsubtilis MJ007, skinny Bacillus
description: <strong>Tilt Series Date:</strong> 2011-08-02</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> MJ007, ponA null</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> strain from Kit Pogliano at UCSD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation media</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-08-02-35/3dimage_24789/</p>mj007_30002_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-08-02-35/3dimage_24789/mj007_30002_full.rec"
        > <i class="download icon"></i> Download </a></p>

        mj007_30002.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-08-02-35/rawdata/mj007_30002.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/jrdg2-0nv94
title: PAOI delta aer2

description: Pseudomonas aeruginosa delta aer2
description: <strong>Tilt Series Date:</strong> 2014-10-15</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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> Kylie Watts</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Streak on LB plates and incubate overnight at 37°C- Inoculate 5 mL MOPS Minimal Media Limited Nitrogen from plate and grow at 30°C for ~24 hours</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2014-10-15-20/rawdata/</p>PAO1DeltaAer2MC0026_mcorr.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.3 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        PAO1DeltaAer2MC0026_mcorr_part121_2.rec,  Reconstruction (Pixel Size 1.28 nm), 688.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/b8gkh-9f644
title: Delftia acidovorans in NB

description: Delftia acidovorans Cs1-4 grown in NB
description: <strong>Tilt Series Date:</strong> 2009-03-30</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Delftia acidovorans</p>
<strong>Strain:</strong> Cs1-4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 0.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> grown by Bill Hickey at UW-Madison; data collected and processed by Elitza Tocheva</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in NB.</p>
<strong>Sample Preparation:</strong> 20nm gold, 2s blot, -2 offset</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-03-30-11/rawdata/</p>09mar30c_WTonNB_021_orig.st,  Tilt Series (Pixel Size 0.962 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09mar30c_WTonNB_021.rec,  Reconstruction (Pixel Size 0.0 nm), 403.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>