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While the contribution of immune cell infiltration and fibroblast activation is recognized, the cellular heterogeneity and the potential role of local microbial dysbiosis in the orbital microenvironment remain poorly defined. Here, we present a multi-omics dataset derived from OA of patients with TED and healthy controls collected at Beijing Tongren Hospital. The dataset comprises single-cell RNA sequencing (scRNA-seq) data generated from human orbital adipose tissue and subcutaneous fat. Following quality control filtering and doublet removal, a total of 61,302 high-quality singlet cells were retained for downstream analyses, capturing the transcriptomic landscape of orbital fibroblasts, immune subsets, and vascular cells. In parallel, 16S rRNA gene sequencing was performed on orbital adipose tissue samples collected from the integrated study cohort, alongside environmental samples for contamination assessment, to characterize the low-biomass orbital microbiome DNA signatures. Raw sequencing reads, quality-controlled gene-expression matrices, and contamination-corrected microbial feature tables are provided. Our dataset provides an opportunity to investigate the crosstalk between host cellular immunity and potential local microbiome signatures, facilitating hypothesis generation regarding host-microbiome crosstalk and the exploration of novel therapeutic targets for TED.<\/jats:p>","DOI":"10.1038\/s41597-026-08064-8","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T12:43:15Z","timestamp":1786624995000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An integrated single-cell transcriptomic and microbiome dataset of orbital adipose tissue in thyroid eye disease"],"prefix":"10.1038","volume":"13","author":[{"given":"Xiang","family":"Xu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiqi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haowen","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingyu","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingming","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"issue":"3","key":"8064_CR1","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1007\/s40123-026-01326-z","volume":"15","author":"C Lei","year":"2026","unstructured":"Lei, C. et al. 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