Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis Article Swipe
Markus Joppich
,
Kami Pekayvaz
,
Sophia Brambs
,
Viktoria Knottenberg
,
Luke Eivers
,
Martin Dichgans
,
Steffen Tiedt
,
Ralf Zimmer
,
Leo Nicolai
,
Konstantin Stark
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.5281/zenodo.10466853
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.5281/zenodo.10466853
Original Data for the manuscript: Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis and correlate with thrombus resolution The manuscript is accessible at https://doi.org/10.1016/j.immuni.2025.03.020 . Please cite the journal publication when using any of this data. Processed scRNA-seq data seurat_humancombined_libintSubsetGroups.Rds -> fully processed Seurat objects objGroups_libint_conditions.tsv -> annotations for main Seurat object integrated_mouse_thrombus.rds -> mouse thrombus dataset arb_obj_integrated.Rds -> ARB Thrombus (Artificial thrombus, Real Thrombus, Blood) Seurat object Original Data (scRNA-seq) pat1_raw_feature_bc_matrix.h5 -> Sample 21053_0001 pat2_raw_feature_bc_matrix.h5 -> Sample 21053_0003 pat3_raw_feature_bc_matrix.h5 -> Sample sample_Thr3 pat4_5_raw_feature_bc_matrix.h5 -> Sample sample_Thr4 pat6_raw_feature_bc_matrix.h5 -> Sample sample_Thr5 pat7_raw_feature_bc_matrix.h5 -> Sample samples_ATTHR mt_raw_feature_bc_matrix.h5 -> Mouse arb_raw_feature_bc_matrix.h5 -> ARB Thrombus (Artificial thrombus, Real Thrombus, Blood) Original Data (bulk) coagulation_classical_counts.tsv coagulation_nonclassical_counts.tsv hypoxia_classical_counts.tsv hypoxia_nonclassical_counts.tsv monocytes_blood_thrombus_counts.tsv neutrophils_blood_thrombus_counts.tsv Original Data (spliced/unspliced by velocyto; matching above sample names): pat1_velocyto.loom -> Sample 21053_0001 pat2_velocyto.loom -> Sample 21053_0003 pat3_velocyto.loom -> Sample sample_Thr3 pat4_5_velocyto.loom -> Sample sample_Thr4 pat6_velocyto.loom -> Sample sample_Thr5 pat7_velocyto.loom -> Sample samples_ATTHR Scripts: functions.R -> script with helper utilities mt_process.R -> script for processing the mouse data process.R -> script for processing the main data set process_de_obj.R -> script for performing DE analysis process_label_transfer.R -> script for doing label transfer between human and mouse dataset and further analyses process_label_transfer.ipynb -> script for doing label transfer between human and mouse dataset and further analyses process_monocle.R -> script for doing monocle-based analyses process_wgcna.R -> script for doing wgcna-based analyses subset_velocities_step1.R -> Seurat to file-based data 2_velocities_monos.py-> Mono-subset velocity analysis 2_velocities_neutros.py -> Neutro-subset velocity analysis analysis_arb_process.ipynb -> Seurat processing of ARB Thrombus
Related Topics
Metadata
- Type
- dataset
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- en
- Landing Page
- https://doi.org/10.5281/zenodo.10466853
- OA Status
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All OpenAlex metadata
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https://openalex.org/W4393814853Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.5281/zenodo.10466853Digital Object Identifier
- Title
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Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosisWork title
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datasetOpenAlex work type
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enPrimary language
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2025Year of publication
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2025-01-01Full publication date if available
- Authors
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Markus Joppich, Kami Pekayvaz, Sophia Brambs, Viktoria Knottenberg, Luke Eivers, Martin Dichgans, Steffen Tiedt, Ralf Zimmer, Leo Nicolai, Konstantin StarkList of authors in order
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https://doi.org/10.5281/zenodo.10466853Publisher landing page
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://doi.org/10.5281/zenodo.10466853Direct OA link when available
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Monocyte, Thrombosis, Biology, Immunology, Medicine, Internal medicineTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| best_oa_location.source.host_organization | https://openalex.org/I67311998 |
| best_oa_location.source.host_organization_name | European Organization for Nuclear Research |
| best_oa_location.source.host_organization_lineage | https://openalex.org/I67311998 |
| best_oa_location.license | cc-by |
| best_oa_location.pdf_url | |
| best_oa_location.version | |
| best_oa_location.raw_type | dataset |
| best_oa_location.license_id | https://openalex.org/licenses/cc-by |
| best_oa_location.is_accepted | False |
| best_oa_location.is_published | False |
| best_oa_location.raw_source_name | |
| best_oa_location.landing_page_url | https://doi.org/10.5281/zenodo.10466853 |
| primary_location.id | doi:10.5281/zenodo.10466853 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S4306400562 |
| primary_location.source.issn | |
| primary_location.source.type | repository |
| primary_location.source.is_oa | True |
| primary_location.source.issn_l | |
| primary_location.source.is_core | False |
| primary_location.source.is_in_doaj | False |
| primary_location.source.display_name | Zenodo (CERN European Organization for Nuclear Research) |
| primary_location.source.host_organization | https://openalex.org/I67311998 |
| primary_location.source.host_organization_name | European Organization for Nuclear Research |
| primary_location.source.host_organization_lineage | https://openalex.org/I67311998 |
| primary_location.license | cc-by |
| primary_location.pdf_url | |
| primary_location.version | |
| primary_location.raw_type | dataset |
| primary_location.license_id | https://openalex.org/licenses/cc-by |
| primary_location.is_accepted | False |
| primary_location.is_published | False |
| primary_location.raw_source_name | |
| primary_location.landing_page_url | https://doi.org/10.5281/zenodo.10466853 |
| publication_date | 2025-01-01 |
| publication_year | 2025 |
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| abstract_inverted_index.Neutro-subset | 238 |
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| abstract_inverted_index.process_de_obj.R | 175 |
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| abstract_inverted_index.Immunothrombolytic | 5 |
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| abstract_inverted_index.pat7_velocyto.loom | 147 |
| abstract_inverted_index.monocyte-neutrophil | 6 |
| abstract_inverted_index.pat4_5_velocyto.loom | 139 |
| abstract_inverted_index.arb_obj_integrated.Rds | 59 |
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| abstract_inverted_index.arb_raw_feature_bc_matrix.h5 | 100 |
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| abstract_inverted_index.pat2_raw_feature_bc_matrix.h5 | 77 |
| abstract_inverted_index.pat3_raw_feature_bc_matrix.h5 | 81 |
| abstract_inverted_index.pat6_raw_feature_bc_matrix.h5 | 89 |
| abstract_inverted_index.pat7_raw_feature_bc_matrix.h5 | 93 |
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| abstract_inverted_index.coagulation_nonclassical_counts.tsv | 113 |
| abstract_inverted_index.monocytes_blood_thrombus_counts.tsv | 116 |
| abstract_inverted_index.neutrophils_blood_thrombus_counts.tsv | 117 |
| abstract_inverted_index.seurat_humancombined_libintSubsetGroups.Rds | 41 |
| abstract_inverted_index.https://doi.org/10.1016/j.immuni.2025.03.020 | 25 |
| cited_by_percentile_year | |
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