{"doi":"10.1038/s42255-023-00876-x","title":"Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas","abstract":"Although multiple pancreatic islet single-cell RNA-sequencing (scRNA-seq) datasets have been generated, a consensus on pancreatic cell states in development, homeostasis and diabetes as well as the value of preclinical animal models is missing. Here, we present an scRNA-seq cross-condition mouse islet atlas (MIA), a curated resource for interactive exploration and computational querying. We integrate over 300,000 cells from nine scRNA-seq datasets consisting of 56 samples, varying in age, sex and diabetes models, including an autoimmune type 1 diabetes model (NOD), a glucotoxicity/lipotoxicity type 2 diabetes model (db/db) and a chemical streptozotocin β-cell ablation model. The β-cell landscape of MIA reveals new cell states during disease progression and cross-publication differences between previously suggested marker genes. We show that β-cells in the streptozotocin model transcriptionally correlate with those in human type 2 diabetes and mouse db/db models, but are less similar to human type 1 diabetes and mouse NOD β-cells. We also report pathways that are shared between β-cells in immature, aged and diabetes models. MIA enables a comprehensive analysis of β-cell responses to different stressors, providing a roadmap for the understanding of β-cell plasticity, compensation and demise.","journal":"Nature Metabolism","year":2023,"id":6835,"datarank":1.486969670686098,"base_score":4.2626798770413155,"endowment":4.2626798770413155,"self_citation_contribution":0.6394019815561974,"citation_network_contribution":0.8475676891299005,"self_endowment_contribution":0.6394019815561974,"citer_contribution":0.8475676891299005,"corpus_percentile":62.08299430431245,"corpus_rank":467,"citation_count":79,"citer_count":70,"citers_with_citation_signal":43,"citers_with_endowment":43,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9137,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-09-11","fair_score":61.25,"fair_percentile":92.70008795074759,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":18912,"name":"Aimée Bastidas-Ponce","orcid":"0000-0002-3117-3591","position":1,"is_corresponding":false},{"id":2919,"name":"Mostafa Bakhti","orcid":"0000-0002-2307-1122","position":2,"is_corresponding":false},{"id":11447,"name":"Luke Zappia","orcid":"0000-0001-7744-8565","position":3,"is_corresponding":false},{"id":3572,"name":"Maren Büttner","orcid":"0000-0002-6189-3792","position":4,"is_corresponding":false},{"id":34882,"name":"Ciro Salinno","orcid":"0000-0003-4364-3236","position":5,"is_corresponding":false},{"id":6097,"name":"Michael Sterr","orcid":null,"position":6,"is_corresponding":false},{"id":6099,"name":"Anika Böttcher","orcid":"0000-0001-5473-3136","position":7,"is_corresponding":false},{"id":18914,"name":"Adriana Migliorini","orcid":"0000-0002-1024-6042","position":8,"is_corresponding":false},{"id":2920,"name":"Heiko Lickert","orcid":"0000-0002-4597-8825","position":9,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":10,"is_corresponding":false},{"id":1696,"name":"Karin Hrovatin","orcid":"0000-0003-3319-9645","position":0,"is_corresponding":true}],"reference_count":179,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"37697055","pmcid":"PMC10513934","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":77.5,"fair_a":80.0,"fair_i":37.5,"fair_r":50.0,"fair_zscore":1.4508,"fair_rationale":{"fair_score":61.25,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":77.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, 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protocol","kind":"llm","weight":1.0,"fraction":1.0,"signal":null,"rationale":"Clear access protocols are given via GEO accession numbers, a GitHub repository, and a cellxgene instance, all publicly accessible under a CC BY 4.0 license."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"Standard formats (GEO, 10x Genomics) and identifiers (Ensembl, GEO) are used, but formal ontologies for cell types or conditions are not explicitly 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machine-readable."}]}},"suggestions":["Embed machine-readable metadata (e.g., JSON-LD) in the paper or as a structured data file to improve findability.","Use standard ontologies (e.g., Cell Ontology) for cell type annotations to enhance interoperability.","Explicitly state the software license (e.g., MIT) for the code repository in the paper.","Provide a data dictionary or schema for metadata tables to facilitate automated reuse.","Make supplementary tables available in machine-readable formats (e.g., CSV) alongside the PDF."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:41:25.978396Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}