{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Vannan A"],"funding":["NHLBI NIH HHS","NHGRI NIH HHS"],"pubmed_abstract":["The human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup of this distal lung is a hallmark of pulmonary fibrosis (PF) and other progressive chronic lung diseases. Single-cell transcriptomic studies have revealed numerous disease-emergent/enriched cell types/states in PF lungs, but the spatial contexts wherein these cells contribute to disease pathogenesis has remained uncertain. Using sub-cellular resolution image-based spatial transcriptomics, we analyzed the gene expression of more than 1 million cells from 19 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characteri"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2023.12.15.571954"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10760144"],"repository":["biostudies-literature"],"pubmed_title":["Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis."],"pmcid":["PMC10760144"],"funding_grant_id":["R01 HG011886","R01 HL126176","K08 HL143051","R01 HL168556","T32 HL094296","P01 HL092870","R01 HL158906","R01 HL145372"],"pubmed_authors":["Ware LB","Blackwell TS","Williams AL","Serezani AP","Kropski JA","Nichols DS","Negretti NM","McCall AS","McCarthy DJ","Vannan A","Walia R","Shim H","Calvi CL","Gokey JJ","Mee ED","Hirsh S","Taylor CJ","Sucre JM","Shaver CM","Hirsh J","Polosukhin VV","Bacchetta MJ","Banovich NE","Lyu R"],"additional_accession":[]},"is_claimable":false,"name":"Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis.","description":"The human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup of this distal lung is a hallmark of pulmonary fibrosis (PF) and other progressive chronic lung diseases. Single-cell transcriptomic studies have revealed numerous disease-emergent/enriched cell types/states in PF lungs, but the spatial contexts wherein these cells contribute to disease pathogenesis has remained uncertain. Using sub-cellular resolution image-based spatial transcriptomics, we analyzed the gene expression of more than 1 million cells from 19 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characteri","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Dec","modification":"2026-04-07T16:18:48.813Z","creation":"2026-04-07T15:15:07.976Z"},"accession":"S-EPMC10760144","cross_references":{"pubmed":["38168317"],"doi":["10.1101/2023.12.15.571954"]}}