{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Chang AC"],"funding":["NHGRI NIH HHS","NCI NIH HHS","NIH HHS"],"pubmed_abstract":["Spatial transcriptomics provides insights into tissue architecture by linking gene expression with spatial localization. Current deconvolution methods rely heavily on single-cell RNA sequencing (scRNA-seq) references, which are costly and often unavailable, mainly if the tissue under evaluation is limited, such as in a core biopsy specimen. We present a novel tool, CITEgeist, that deconvolutes spatial transcriptomics data using antibody capture from the same slide as the reference, directly leveraging cell surface protein measurements from the same tissue section. This approach circumvents the limitations of scRNA-seq as a reference, offering a cost-effective and biologically grounded alternative. Our method employs mathematical optimization to estimate cell type proportions and gene expre"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2025.02.15.638331"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11870549"],"repository":["biostudies-literature"],"pubmed_title":["CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends."],"pmcid":["PMC11870549"],"funding_grant_id":["P30 CA047904","S10 OD028483","R01 HG010589","F30 CA264963"],"pubmed_authors":["Schwartz R","Lee AV","Chang AC","Schlegel BT","Carleton N","McAuliffe PF","Oesterreich S"],"additional_accession":[]},"is_claimable":false,"name":"CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends.","description":"Spatial transcriptomics provides insights into tissue architecture by linking gene expression with spatial localization. Current deconvolution methods rely heavily on single-cell RNA sequencing (scRNA-seq) references, which are costly and often unavailable, mainly if the tissue under evaluation is limited, such as in a core biopsy specimen. We present a novel tool, CITEgeist, that deconvolutes spatial transcriptomics data using antibody capture from the same slide as the reference, directly leveraging cell surface protein measurements from the same tissue section. This approach circumvents the limitations of scRNA-seq as a reference, offering a cost-effective and biologically grounded alternative. Our method employs mathematical optimization to estimate cell type proportions and gene expre","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Feb","modification":"2026-05-27T03:15:51.307Z","creation":"2025-07-04T03:05:37.15Z"},"accession":"S-EPMC11870549","cross_references":{"pubmed":["40027773"],"doi":["10.1101/2025.02.15.638331"]}}