{"doi":"10.1101/2024.04.22.590125","title":"Tissue and cellular spatiotemporal dynamics in colon aging","abstract":"<h4>ABSTRACT</h4> Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ∼1,500 mouse gut tissues profiled by spatial transcriptomics and ∼400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.","journal":null,"year":2024,"id":6399,"datarank":0.21591795285302995,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.007973798685046317,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.007973798685046317,"corpus_percentile":44.83319772172498,"corpus_rank":679,"citation_count":3,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6324,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-04-26","fair_score":39.1667,"fair_percentile":19.854881266490764,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":58922,"name":"Francesco Cambuli","orcid":null,"position":1,"is_corresponding":false},{"id":475,"name":"Tarmo Äijö","orcid":"0000-0002-3008-4634","position":2,"is_corresponding":false},{"id":18735,"name":"Britta Lötstedt","orcid":"0000-0003-3545-5489","position":3,"is_corresponding":false},{"id":28702,"name":"Nemanja Despot Marjanovic","orcid":null,"position":4,"is_corresponding":false},{"id":7477,"name":"Olena Kuksenko","orcid":"0000-0002-1728-4957","position":5,"is_corresponding":false},{"id":58924,"name":"Matthew Smith-Erb","orcid":null,"position":6,"is_corresponding":false},{"id":59169,"name":"Sara Fernandez","orcid":null,"position":7,"is_corresponding":false},{"id":58925,"name":"Daniel Domovic","orcid":"0000-0003-4576-7988","position":8,"is_corresponding":false},{"id":16531,"name":"Nicholas Van Wittenberghe","orcid":"0000-0002-7653-9729","position":9,"is_corresponding":false},{"id":16530,"name":"Eugene Drokhlyansky","orcid":"0000-0002-1939-3559","position":10,"is_corresponding":false},{"id":18917,"name":"Gabriel K. Griffin","orcid":"0000-0002-4042-6757","position":11,"is_corresponding":false},{"id":58926,"name":"Hemali Phatnani","orcid":"0000-0002-6571-3891","position":12,"is_corresponding":false},{"id":476,"name":"Richard Bonneau","orcid":"0000-0003-4354-7906","position":13,"is_corresponding":false},{"id":29633,"name":"Prisca Liberali","orcid":"0000-0003-0695-6081","position":14,"is_corresponding":false},{"id":483,"name":"Sanja Vicković","orcid":"0000-0003-0985-9885","position":17,"is_corresponding":false},{"id":58921,"name":"Aidan C. Daly","orcid":"0000-0003-4447-8623","position":0,"is_corresponding":true}],"reference_count":160,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"38712088","pmcid":"PMC11071407","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"green","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":80.0,"fair_a":60.0,"fair_i":0.0,"fair_r":16.6667,"fair_zscore":-0.5468,"fair_rationale":{"fair_score":39.17,"has_llm":false,"dimensions":{"F":{"name":"Findable","score":80.0,"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, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null}]},"A":{"name":"Accessible","score":60.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null}]},"I":{"name":"Interoperable","score":0.0,"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}]},"R":{"name":"Reusable","score":16.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null}]}},"suggestions":["Attach a clear, open reuse license (e.g. CC-BY or CC0).","Provide a direct, free link to the full text or data files.","Link the underlying datasets via DOIs / DataCite relations.","Reference data using standard accessions (e.g. GEO, PDB, ClinicalTrials.gov).","Maintain explicit versioning for the dataset."],"model":null,"agent_version":"fair_agent_v1","fulltext_source":"epmc_xml"},"fair_model":null,"fair_agent_version":"fair_agent_v1","fair_fulltext_source":"epmc_xml","fair_has_llm":false,"fair_computed_at":"2026-06-17T22:59:54.597426Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}