cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12633638
title: Dataset related to article "Single-Cell and Single-Nucleus Multiomics Reveal Cardiac Endothelial Cell Heterogeneity and Novel Pathological Processes in Pressure Overload-Induced Hypertrophy"

description: This record contains raw data related to article “Single-Cell and Single-Nucleus Multiomics Reveal Cardiac Endothelial Cell Heterogeneity and Novel Pathological Processes in Pressure Overload-Induced Hypertrophy"

Endothelial cells, the most prevalent cellular population in the heart, line the internal walls of coronary and lymphatic vessels and form the endocardium and cardiac valves. The heterogeneity of cardiac endothelium poses a challenge in fully understanding endothelial states. However, to better grasp the plasticity of endothelial cell phenotypes, it's crucial to distinguish the varied responses of endothelial populations to physiological and pathological stimuli. Endothelial dysfunction plays a significant role in the development and progression of heart failure, a condition impacting millions globally. For the heart to sustain pressure-overload-induced remodelling, endothelial cells must proliferate and generate new blood vessels. When cardiomyocyte hypertrophy and angiogenesis become uncoupled, it leads to decompensated heart failure. Despite this, the molecular mechanisms governing cardiac vascularization during pathological hypertrophy remain unclear.

Transcriptional phenotyping methods have been widely used to capture endothelial cell plasticity and heterogeneity. However, only single-cell profiling has effectively resolved distinct phenotypes. While single-cell RNA sequencing can create detailed cellular maps and cell-to-cell communication networks, it does not fully elucidate how gene regulatory programs are established or how cell states, functions, and responses are specified. To address these gaps, multimodal omics approaches have been developed, allowing for simultaneous profiling of chromatin accessibility and gene expression within the same cell.

In our study, we aimed to characterize the transcriptional and epigenetic profiles of cardiac endothelial cells in a mouse model of pressure-overload-induced hypertrophy using multiomics bioinformatic approaches at single-cell resolution. This innovative technology enabled us to uncover the regulatory mechanisms that drive endothelial cell sub-population specifications following banding. Our resulting atlas is intended to serve as a valuable reference and resource for future studies and the development of therapeutic strategies targeting endothelial cells in cardiovascular diseases.
DOI: 10.5281/zenodo.12633639
title: Dataset related to article "Single-Cell and Single-Nucleus Multiomics Reveal Cardiac Endothelial Cell Heterogeneity and Novel Pathological Processes in Pressure Overload-Induced Hypertrophy"

description: This record contains raw data related to article “Single-Cell and Single-Nucleus Multiomics Reveal Cardiac Endothelial Cell Heterogeneity and Novel Pathological Processes in Pressure Overload-Induced Hypertrophy"

Endothelial cells, the most prevalent cellular population in the heart, line the internal walls of coronary and lymphatic vessels and form the endocardium and cardiac valves. The heterogeneity of cardiac endothelium poses a challenge in fully understanding endothelial states. However, to better grasp the plasticity of endothelial cell phenotypes, it's crucial to distinguish the varied responses of endothelial populations to physiological and pathological stimuli. Endothelial dysfunction plays a significant role in the development and progression of heart failure, a condition impacting millions globally. For the heart to sustain pressure-overload-induced remodelling, endothelial cells must proliferate and generate new blood vessels. When cardiomyocyte hypertrophy and angiogenesis become uncoupled, it leads to decompensated heart failure. Despite this, the molecular mechanisms governing cardiac vascularization during pathological hypertrophy remain unclear.

Transcriptional phenotyping methods have been widely used to capture endothelial cell plasticity and heterogeneity. However, only single-cell profiling has effectively resolved distinct phenotypes. While single-cell RNA sequencing can create detailed cellular maps and cell-to-cell communication networks, it does not fully elucidate how gene regulatory programs are established or how cell states, functions, and responses are specified. To address these gaps, multimodal omics approaches have been developed, allowing for simultaneous profiling of chromatin accessibility and gene expression within the same cell.

In our study, we aimed to characterize the transcriptional and epigenetic profiles of cardiac endothelial cells in a mouse model of pressure-overload-induced hypertrophy using multiomics bioinformatic approaches at single-cell resolution. This innovative technology enabled us to uncover the regulatory mechanisms that drive endothelial cell sub-population specifications following banding. Our resulting atlas is intended to serve as a valuable reference and resource for future studies and the development of therapeutic strategies targeting endothelial cells in cardiovascular diseases.
DOI: 10.15468/dl.zy9xk4
title: Occurrence Download

description: A dataset containing 328003 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Lao People’s Democratic Republic",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 328003 records from 705 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002949-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.7743777
title: CA-discharge data set, scripts and raw data

description: Gauge locations of 295 gauges in Central Asia, including long-term norm discharge, basin outlines and basin characteristics compiled from 3rd-party data. Discharge time series for 135 gauge locations collected from the hydrological yearbooks of Hydrometeorological Organisations in Central Asia. 

Instructions of how to use the data can be found in the readme document in the folder CA-data-paper-scripts. 

! Important note: Please do not use the glacier thinning rates extracted from Hugonnet et al., 2021 (https://doi.org/10.1038/s41586-021-03436-z), i.e. features gl_dmdt_km3a and gl_dmdtda_mma. The ice density is not accounted for in our averages.
DOI: 10.5281/zenodo.8147591
title: CA-discharge data set, scripts and raw data

description: Gauge locations of 295 gauges in Central Asia, including long-term norm discharge, basin outlines and basin characteristics compiled from 3rd-party data. Discharge time series for 135 gauge locations collected from the hydrological yearbooks of Hydrometeorological Organisations in Central Asia. 

Instructions of how to use the data can be found in the readme document in the folder CA-data-paper-scripts. 

! Important note: Please do not use the glacier thinning rates extracted from Hugonnet et al., 2021 (https://doi.org/10.1038/s41586-021-03436-z), i.e. features gl_dmdt_km3a and gl_dmdtda_mma. The ice density is not accounted for in our averages.
DOI: 10.15468/dl.deyeaz
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Juglans nigra",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 124 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000313-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5k4w5d
title: Occurrence Download

description: A dataset containing 648 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Elevation 0.0-0.0m",
 "Geometry POLYGON((11.40173 35.04704,16.39126 35.04704,16.39126 39.50879,11.40173 39.50879,11.40173 35.04704))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 648 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000314-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j43y7p
title: Occurrence Download

description: A dataset containing 564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (May, June, July, August, September, October)",
 "OccurrenceStatus is Present",
 "TaxonKey is Bubalus bubalis",
 "Year 2017-2017"
 ]
}

 The dataset includes 564 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000316-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z5x78m
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xysmalobium membraniferum"
 ]
}

 The dataset includes 10 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000317-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2e38mc
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amphistegina lobifera",
 "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 39 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000319-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.338rx2
title: Occurrence Download

description: A dataset containing 4269922 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Saimiri sciureus, Saissetia oleae, Salmo salar, Salmo trutta, Salvator merianae, Salvatoria clavata, Salvelinus fontinalis, Salvelinus namaycush, Sander lucioperca, Sarasinula plebeia, Sarotherodon melanotheron, Sarotherodon occidentalis, Saurida undosquamis, Scantius aegyptius, Scapharca inaequivalvis, Scaptodrosophila latifasciaeformis, Scardinius erythrophthalmus, Sceliphron caementarium, Sceliphron curvatum, Schizoporella errata)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 4269922 records from 1024 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000284-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r3w7ev
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Colutea arborescens",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 63 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050032-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/3ejcp-mfa31
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 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/dga2018-08-29-223/rawdata/</p>JV9082_201808290223.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-223/rawdata/JV9082_201808290223.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290223_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-223/3dimage_96847/JV9082_201808290223_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/427ex-jq241
title: JV9082_K3_janelia

description: JV9082:DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2019-12-02</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 90.0 eV/Å²,  defocus: -2.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> SerialEM</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.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Data collected at Janelia Krios (K3 camera). Mag: 26000, pixel size: 2.61A. Defocus range -2 to -4 um.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-60/rawdata/</p>9082_Box1_No1_S160.mrc,  Tilt Series (Pixel Size 0.261 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-60/rawdata/9082_Box1_No1_S160.mrc"
        > <i class="download icon"></i> Download </a></p>

        9082_Box1_No1_S160_full.rec,  Reconstruction (Pixel Size 1.044 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2019-12-02-60/3dimage_112597/9082_Box1_No1_S160_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/nj5jc-64626
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 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/dga2018-08-29-389/rawdata/</p>JV9082_20180901a0163.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-389/rawdata/JV9082_20180901a0163.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_20180901a0163_part37_15.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-389/3dimage_97094/JV9082_20180901a0163_part37_15.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7qh69-4yv64
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</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: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </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.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 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/dga2018-08-29-7/rawdata/</p>JV9082_201808290045.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-7/rawdata/JV9082_201808290045.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290045_full.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-7/3dimage_96309/JV9082_201808290045_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/k21ka-bet49
title: BacillusSubtilis_328_4hr

description: This is Bacillus Subtilis tomograms PonA mutant strain 328 (obtained from Amit in Sigal Ben  .  Yehuda lab at the Hebrew university). The idea is to image bacterial nanotubes in Bacilus .  Subtilis.
description: <strong>Tilt Series Date:</strong> 2020-02-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> AB328, ΔponA ΔymdB amyE::ymdB Δhag</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> None</p>
<strong>Collaborators and Roles:</strong> The samples were prepared with Amit and Ritesh (from Sigal Ben Yehuda and Ilan Rosenshine . labs at the Hebrew University). These Samples were incubated for four hours on grids on plates . (I will write the details on my Labjournal).  </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Samples were grown on the grids on agar plates for four hours. Detailed description is in the lab . journal. Yuxi helped in the sample preparation and data collection.</p>
<strong>Sample Preparation:</strong> Samples were taken from the agar plates and washed few times in PBS. Then they were blotted . and plunge-frozen.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-11/rawdata/</p>Bsubtilis_328_4hr_conventional6.mrc,  Tilt Series (Pixel Size 0.449 nm), 518.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-11/rawdata/Bsubtilis_328_4hr_conventional6.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bsubtilis_328_4hr_conventional6.mrc.mdoc,  6.5 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-08-11/rawdata/Bsubtilis_328_4hr_conventional6.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>