{"doi":"10.1101/2021.03.11.434985","title":"Spatial Epigenome Sequencing at Tissue Scale and Cellular Level","abstract":"Abstract Spatial biology is emerging as a new frontier of biomedical research in development and disease, but currently limited to transcriptome and a panel of proteins. Here we present spatial epigenome profiling for three histone modifications (H3K27me3, H3K4me3, H3K27ac) via next-generation sequencing by combining in-tissue CUT&Tag chemistry and microfluidic deterministic barcoding. Spatial chromatin states in mouse embryos or olfactory bulbs revealed tissue type-specific epigenetic regulations, in concordance with ENCODE reference data, but providing spatially resolved genome-wide profiles at tissue scale. Using fluorescence imaging to identify the tissue pixels (20μm) each containing one nucleus allowed us to extract single-cell epigenomes in situ. Spatial chromatin state profiling in tissue may enable unprecedented opportunities to study epigenetic regulation, cell function and fate decision in normal physiology and pathogenesis.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":213487,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":20,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.922,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":805297,"name":"Di Zhang","orcid":"0000-0001-8466-9868","position":1,"is_corresponding":false},{"id":553568,"name":"Yang Liu","orcid":"0000-0003-1830-948X","position":2,"is_corresponding":false},{"id":102742,"name":"Graham Su","orcid":"0000-0002-4170-0180","position":3,"is_corresponding":false},{"id":553569,"name":"Archibald Enninful","orcid":"0000-0002-6350-6530","position":4,"is_corresponding":false},{"id":102747,"name":"Zhiliang Bai","orcid":"0000-0002-3977-3057","position":5,"is_corresponding":false},{"id":35664,"name":"Rong Fan","orcid":"0000-0001-7805-8059","position":6,"is_corresponding":false},{"id":102741,"name":"Yanxiang Deng","orcid":"0000-0002-9975-8086","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-18T23:52:36.886828Z","pmid":null,"pmcid":null,"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":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}