cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29988511
title: DMG single cell regulatory networks

description: Context-specific regulatory networks—consisting of bivariate transcriptional regulatory interactions between a set of predefined putative transcriptional regulators and potential transcriptional targets—were reverse engineered using the ARACNe-AP algorithm (publicly available at github.com/califano-lab/ARACNe-AP). Candidate transcriptional regulators (available at github.com/califano-lab/tf_cotf_signalling_list) included 1,813 transcription factors (genes annotated in the Gene Ontology Molecular Function database (GO) as GO:0003700—‘DNA binding transcription factor activity’, or as GO: :0003677—‘DNA binding’ and GO:0030528—‘Transcription regulator activity’, or as GO:0003677 and GO:0045449—‘Regulation of transcription’), 969 transcriptional co-factors (a manually curated list, not overlapping with the transcription factor list, built upon genes annotated as GO:0003712—‘transcription cofactor activity’ or GO:0030528 or GO:0045449) or 3,370 signaling-pathway-related genes (annotated in the GO Biological Process database as GO:0007165—‘signal transduction’ and in the GO Cellular Component database as GO:0005622—‘intracellular’ or GO:0005886—‘plasma membrane’). Standard parameters were set including zero DPI (Data Processing Inequality) tolerance and MI (Mutual Information) p-value threshold of 10-8, computed by permuting the original dataset as a null model.For tumor compartment-specific analyses, DMG tumor networks were generated using the log2(CPM/10+1) normalized gene expression counts for tumor cells for each of the six patients individually. This resulted in 1,440 regulators, 5,118 targets and 72,000 interactions for BCH1126; 2,469 regulators, 7,088 targets and 123,450 interactions for BCH836; 2,045 regulators, 6,343 targets and 102,250 interactions for BCH869; 1,117 regulators, 4,558 targets and 55,850 interactions for MUV1; 714 regulators, 4,505 targets and 35,700 interactions for MUV10; and 2,281 regulators, 7,007 targets and 114,050 interactions for MUV5.
DOI: 10.6084/m9.figshare.29988511.v1
title: DMG single cell regulatory networks

description: Context-specific regulatory networks—consisting of bivariate transcriptional regulatory interactions between a set of predefined putative transcriptional regulators and potential transcriptional targets—were reverse engineered using the ARACNe-AP algorithm (publicly available at github.com/califano-lab/ARACNe-AP). Candidate transcriptional regulators (available at github.com/califano-lab/tf_cotf_signalling_list) included 1,813 transcription factors (genes annotated in the Gene Ontology Molecular Function database (GO) as GO:0003700—‘DNA binding transcription factor activity’, or as GO: :0003677—‘DNA binding’ and GO:0030528—‘Transcription regulator activity’, or as GO:0003677 and GO:0045449—‘Regulation of transcription’), 969 transcriptional co-factors (a manually curated list, not overlapping with the transcription factor list, built upon genes annotated as GO:0003712—‘transcription cofactor activity’ or GO:0030528 or GO:0045449) or 3,370 signaling-pathway-related genes (annotated in the GO Biological Process database as GO:0007165—‘signal transduction’ and in the GO Cellular Component database as GO:0005622—‘intracellular’ or GO:0005886—‘plasma membrane’). Standard parameters were set including zero DPI (Data Processing Inequality) tolerance and MI (Mutual Information) p-value threshold of 10-8, computed by permuting the original dataset as a null model.For tumor compartment-specific analyses, DMG tumor networks were generated using the log2(CPM/10+1) normalized gene expression counts for tumor cells for each of the six patients individually. This resulted in 1,440 regulators, 5,118 targets and 72,000 interactions for BCH1126; 2,469 regulators, 7,088 targets and 123,450 interactions for BCH836; 2,045 regulators, 6,343 targets and 102,250 interactions for BCH869; 1,117 regulators, 4,558 targets and 55,850 interactions for MUV1; 714 regulators, 4,505 targets and 35,700 interactions for MUV10; and 2,281 regulators, 7,007 targets and 114,050 interactions for MUV5.
DOI: 10.22002/phr5k-a6e20
title: T6S sheath (recombinant) preparation

description: 2011_08_07_
description: <strong>Tilt Series Date:</strong> 2011-08-07</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> T6S sheath (recombinant) preparation</p>
<strong>Strain:</strong> V. cholera 2740-80 in E. coli</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: °, constant angular increment, dosage: 0.0 eV/Å²,  defocus: 0.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> Mekalanos</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-08-07-8/rawdata/</p>2011_08_07_V29_0008.mrc,  Tilt Series (Pixel Size 0.0 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-08-07-8/rawdata/2011_08_07_V29_0008.mrc"
        > <i class="download icon"></i> Download </a></p>

        2011_08_07_V29_0008_part.rec,  Reconstruction (Pixel Size 0.0 nm), 825.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-08-07-8/3dimage_34952/2011_08_07_V29_0008_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/s4y96-06c63
title: sporulating MJ007 t=2.5

description: MJ007t=2.5
description: <strong>Tilt Series Date:</strong> 2009-07-30</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> Leginon</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> sporulation medium</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/etl2009-07-30-1/rawdata/</p>09jul29a_007t2.5_001.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/etl2009-07-30-1/rawdata/09jul29a_007t2.5_001.mrc"
        > <i class="download icon"></i> Download </a></p>

        cell1_full.rec,  Reconstruction (Pixel Size 1.9 nm), 708.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-07-30-1/3dimage_25951/cell1_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/p9f2c-rzh25
title: Vibrio cholerae 2740-80

description: 11apr03d_6
description: <strong>Tilt Series Date:</strong> 2011-04-03</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Vibrio cholerae 2740-80</p>
<strong>Strain:</strong> mutant dVCA0108</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: °, constant angular increment, dosage: 0.0 eV/Å²,  defocus: 0.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> Mekalanos</p>
  mpa2011-04-03-22_slicer7599.jpg: Pillus
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-04-03-22/rawdata/</p>11apr03d_VC5_006.mrc,  Tilt Series (Pixel Size 0.0 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-04-03-22/rawdata/11apr03d_VC5_006.mrc"
        > <i class="download icon"></i> Download </a></p>

        11apr03d_VC5_006_part.rec,  Reconstruction (Pixel Size 0.0 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-04-03-22/3dimage_34663/11apr03d_VC5_006_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/rndxf-4s882
title: M222R chemoreceptor mutant

description: M222R HAMP mutant locked in 'CHeA inactivating state'
description: <strong>Tilt Series Date:</strong> 2010-03-19</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </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: 34000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> John Parkinson </p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in TB medium, induced with salycilate (0.6 µM) for three hours, then penicillin treated for one hour </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-03-19-4/rawdata/</p>10mar19a_EcoliM222K_004.st,  Tilt Series (Pixel Size 0.632 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-03-19-4/rawdata/10mar19a_EcoliM222K_004.st"
        > <i class="download icon"></i> Download </a></p>

        10mar19a_EcoliM222K_004.rec,  Reconstruction (Pixel Size 0.632 nm), 62.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-03-19-4/3dimage_12785/10mar19a_EcoliM222K_004.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/54qrd-y3j20
title: C65_HuvecspNL24h_11122012

description: Whole cells were grown on Au finder grids and infected with pNLGFP. Sample frozen 24h post infection
description: <strong>Tilt Series Date:</strong> 2011-11-12</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: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: None μm,  magnification: 22500x. </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> pNLGFP proviral construct provided by Irvin Chen UCLA</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-11-12-47/rawdata/</p>12nov10_C65_HuvecspNL24h_AT2aBT10013.mrc,  Tilt Series (Pixel Size 0.45 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-11-12-47/rawdata/12nov10_C65_HuvecspNL24h_AT2aBT10013.mrc"
        > <i class="download icon"></i> Download </a></p>

        12nov10_C65_HuvecspNL24h_AT2aBT10013_full.rec,  Reconstruction (Pixel Size 1.8 nm), 530.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-11-12-47/3dimage_23399/12nov10_C65_HuvecspNL24h_AT2aBT10013_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/rbeb3-z9m14
title: Caulobacter 10mM Galactose 10sec

description: CB15N Caulobacter cells after 10sec exposure to Galactose
description: <strong>Tilt Series Date:</strong> 2010-01-06</p>
<strong>Data Taken By:</strong> Ariane Briegel</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: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
  aba2010-01-06-8_slicer5580.jpg: flat vesicle aba2010-01-06-8_slicer5581.jpg: filaments aba2010-01-06-8_slicer5582.jpg: two layered peptidoglycan
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-01-06-8/rawdata/</p>10jan06a_CB15NGal10sec_009.st,  Tilt Series (Pixel Size 0.632 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-01-06-8/rawdata/10jan06a_CB15NGal10sec_009.st"
        > <i class="download icon"></i> Download </a></p>

        10jan06a_CB15NGal10sec_009.rec,  Reconstruction (Pixel Size 0.0 nm), 252.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-01-06-8/3dimage_12944/10jan06a_CB15NGal10sec_009.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.q8qdsd
title: Occurrence Download

description: A dataset containing 16165 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is one of (EOD – eBird Observation Dataset, iNaturalist Research-grade Observations)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Geometry POLYGON((-80.4399 43.45367,-80.37948 43.45367,-80.37948 43.4859,-80.4399 43.4859,-80.4399 43.45367))"
 ]
}

 The dataset includes 16165 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047053-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/3aerf-grg60
title: CB15N, 0.1mM Galactose,high salt

description: Raw data files of CB15N, 0.1mM Galactose,high salt
description: <strong>Tilt Series Date:</strong> 2009-10-22</p>
<strong>Data Taken By:</strong> Ariane Briegel</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: °, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 27500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> synchronized in 20x M2 salts, 0.1mM Galactose</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2009-10-22-18/rawdata/</p>09oct22a_MT310Auglu50_019.st,  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/aba2009-10-22-18/rawdata/09oct22a_MT310Auglu50_019.st"
        > <i class="download icon"></i> Download </a></p>

        09oct22a_MT310Auglu50_019.rec,  Reconstruction (Pixel Size 1.548 nm), 218.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2009-10-22-18/3dimage_8866/09oct22a_MT310Auglu50_019.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/thhzm-v1d44
title: CB15N, 0.1mM Galactose,high salt

description: Raw data files of CB15N, 0.1mM Galactose,high salt
description: <strong>Tilt Series Date:</strong> 2009-10-22</p>
<strong>Data Taken By:</strong> Ariane Briegel</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: °, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 27500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Purification / Growth Conditions / Treatment:</strong> synchronized in 20x M2 salts, 0.1mM Galactose</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2009-10-22-1/rawdata/</p>Swarmer0_1mM_2.st,  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/aba2009-10-22-1/rawdata/Swarmer0_1mM_2.st"
        > <i class="download icon"></i> Download </a></p>

        Swarmer0_1mM_2.rec,  Reconstruction (Pixel Size 1.548 nm), 188.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2009-10-22-1/3dimage_8832/Swarmer0_1mM_2.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.c5hfp8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centrocercus minimus",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047054-250811113504898/datasets/export for details.
DOI: 10.22002/s9vq8-8ps27
title: E. coli (pLE6, 20 um IPTG)

description: e. coli from Larry Rothfield containing plasmid carrying WT MreB.
description: <strong>Tilt Series Date:</strong> 2011-07-29</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </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>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Sample Preparation:</strong> Induced with 20um IPTG for 2 hours starting at OD600=0.2.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2011-07-29-7/3dimage_44261/</p>20110729_ple6_20umIPTG_20010_full.rec,  Reconstruction (Pixel Size 1.892 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2011-07-29-7/3dimage_44261/20110729_ple6_20umIPTG_20010_full.rec"
        > <i class="download icon"></i> Download </a></p>

        20110729_ple6_20umIPTG_20010.mrc,  Tilt Series (Pixel Size 0.946 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2011-07-29-7/rawdata/20110729_ple6_20umIPTG_20010.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ywbz0-w7473
title: Vibrio cholerae

description: 2011_05_24_
description: <strong>Tilt Series Date:</strong> 2011-05-24</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> 2740-80</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (0.0°, 0.0°), step: °, constant angular increment, dosage: 0.0 eV/Å²,  defocus: 0.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> Mekalanos</p>
  mpa2011-05-24-6_slicer7263.jpg: vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-05-24-6/rawdata/</p>2011_05_24_8.mrc,  Tilt Series (Pixel Size 0.0 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-05-24-6/rawdata/2011_05_24_8.mrc"
        > <i class="download icon"></i> Download </a></p>

        2011_05_24_8_full.rec,  Reconstruction (Pixel Size 0.0 nm), 1.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2011-05-24-6/3dimage_34850/2011_05_24_8_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.11186619
title: Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis - Dataset

description: Recent technological developments have made it possible to map the spatial organization of a tissue at the single-cell resolution. However, computational methods for analyzing spatially continuous variations in tissue microenvironment are still lacking. Here we present ONTraC as a strategy that constructs niche trajectories using a graph neural network-based modeling framework. Our benchmark analysis shows that ONTraC performs more favorably than existing methods for reconstructing spatial trajectories. Applications of ONTraC to public spatial transcriptomics datasets successfully recapitulated the underlying anatomical structure, and further enabled detection of tissue microenvironment-dependent changes in gene regulatory networks and cell-cell interaction activities during embryonic development. Taken together, ONTraC provides a useful and generally applicable tool for the systematic characterization of the structural and functional organization of tissue microenvironments.
DOI: 10.5281/zenodo.16951007
title: Characterizing Spatially Continuous Variations in Tissue Microenvironment through Niche Trajectory Analysis - Dataset

description: Recent technological developments have made it possible to map the spatial organization of a tissue at the single-cell resolution. However, computational methods for analyzing spatially continuous variations in tissue microenvironment are still lacking. Here we present ONTraC as a strategy that constructs niche trajectories using a graph neural network-based modeling framework. Our benchmark analysis shows that ONTraC performs more favorably than existing methods for reconstructing spatial trajectories. Applications of ONTraC to public spatial transcriptomics datasets successfully recapitulated the underlying anatomical structure, and further enabled detection of tissue microenvironment-dependent changes in gene regulatory networks and cell-cell interaction activities during embryonic development. Taken together, ONTraC provides a useful and generally applicable tool for the systematic characterization of the structural and functional organization of tissue microenvironments.