{"doi":"10.1016/j.celrep.2024.115091","title":"Transcriptional profile of the rat cardiovascular system at single-cell resolution","abstract":"We sought to characterize cellular composition across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We performed single-nucleus RNA sequencing (snRNA-seq) in 78 samples in 10 distinct regions, including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins, which produced 505,835 nuclei. We identified 26 distinct cell types and additional subtypes, with different cellular composition across cardiac regions and tissue-specific transcription for each cell type. Several cell subtypes were region specific, including a subtype of vascular smooth muscle cells enriched in the large vasculature. We observed tissue-enriched cellular communication networks, including heightened Nppa-Npr1/2/3 signaling in the sinoatrial node. The existence of tissue-restricted cell types suggests regional regulation of cardiovascular physiology. Our detailed transcriptional characterization of each cell type offers the potential to identify novel therapeutic targets and improve preclinical models of cardiovascular disease.","journal":"Cell Reports","year":2024,"id":427637,"datarank":0.49521589135851035,"base_score":2.772588722239781,"endowment":2.772588722239781,"self_citation_contribution":0.41588830833596724,"citation_network_contribution":0.0793275830225431,"self_endowment_contribution":0.41588830833596724,"citer_contribution":0.0793275830225431,"corpus_percentile":61.29032258064516,"corpus_rank":5005,"citation_count":15,"citer_count":15,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7048,"is_data_producer":true,"deposit_databanks":{"GEO":["GSE280111"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":79604,"name":"Stephen J. Fleming","orcid":"0000-0002-1885-4405","position":1,"is_corresponding":false},{"id":1227229,"name":"Ling Xiao","orcid":"0000-0003-3025-467X","position":2,"is_corresponding":false},{"id":295756,"name":"Amelia Weber Hall","orcid":"0000-0002-7915-0313","position":3,"is_corresponding":false},{"id":551631,"name":"Amer-Denis Akkad","orcid":"0000-0001-6266-947X","position":4,"is_corresponding":false},{"id":24654,"name":"Mark Chaffin","orcid":"0000-0002-1234-5562","position":5,"is_corresponding":false},{"id":902871,"name":"Kayla J. Bendinelli","orcid":"0000-0002-4072-9002","position":6,"is_corresponding":false},{"id":53932,"name":"Nathan R. Tucker","orcid":"0000-0002-5071-4218","position":7,"is_corresponding":false},{"id":552920,"name":"Irinna Papangeli","orcid":null,"position":8,"is_corresponding":false},{"id":1015148,"name":"Helene Mantineo","orcid":null,"position":9,"is_corresponding":false},{"id":738685,"name":"Patricio Flores-Bringas","orcid":"0009-0005-2611-7463","position":10,"is_corresponding":false},{"id":79606,"name":"Mehrtash Babadi","orcid":"0000-0003-1829-8397","position":11,"is_corresponding":false},{"id":551633,"name":"Christian M. Stegmann","orcid":"0000-0001-7573-8948","position":12,"is_corresponding":false},{"id":37053,"name":"Guillermo García‐Cardeña","orcid":"0000-0003-2663-3706","position":13,"is_corresponding":false},{"id":895,"name":"Mark E. Lindsay","orcid":"0000-0001-6724-7938","position":14,"is_corresponding":false},{"id":865228,"name":"Carla Klattenhoff","orcid":null,"position":15,"is_corresponding":false},{"id":896,"name":"Patrick T. Ellinor","orcid":"0000-0002-2067-0533","position":16,"is_corresponding":false},{"id":551632,"name":"Alessandro Arduini","orcid":"0000-0002-0038-8741","position":0,"is_corresponding":true}],"reference_count":89,"raw_metadata":null,"created_at":"2026-07-19T01:58:52.576447Z","pmid":"39709602","pmcid":"PMC11781962","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":61.1111,"fair_a":81.25,"fair_i":40.0,"fair_r":25.0,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"GSE280111","grounded":true,"rationale":"The paper provides a GEO accession, which is a persistent identifier scheme.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Raw FASTQ and h5 count matrix snRNA-seq data have been deposited at GEO","grounded":true,"rationale":"The paper names GEO, a recognised repository, as the holder of the data.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Raw FASTQ and h5 count matrix snRNA-seq data have been deposited at GEO and are publicly available as of the date of publication. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No reuse license is stated for the data; the CC BY-NC-ND license applies to the article only.","gain":16.67,"priority":"essential","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. 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Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"GSE280111","why":"The dataset identifier (GEO accession) appears only in the key resources table (body text), not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No version token or date is given to pin a specific snapshot of the data. [majority verdict 'no' (3/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Raw FASTQ and h5 count matrix snRNA-seq data have been deposited at GEO and are publicly available as of the date of publication. Processed, annotated AnnData h5ad data have been deposited at the Single Cell Portal and are publicly available as of the date of publication. Accession numbers are listed in the key resources table.","why":"The statement points to named repositories (GEO, Single Cell Portal) with accessions, meeting Colavizza category 3. 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Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"We collected 89 samples from 10 regions of the heart and major blood vessels: left ventricle (LV), right ventricle (RV), left atrium (LA), right atrium (RA), septum (base and apex), atrioventricular node (AVN), sinoatrial node (SAN), pulmonary vein (PV), pulmonary artery (PA), and aorta (Ao) (Figure 1A).","why":"The dataset's content (samples, regions, nuclei count) is described in running prose; there is no itemised inventory or section heading for the data files. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:06:45.377056Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}