{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["5(7)"],"submitter":["Reyes-Gopar H"],"pubmed_abstract":["Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. The quantification of locus-specific TE expression in scRNA-seq experiments is challenging due to their repetitive sequence content and poorly characterized annotations. Here, we developed a computational tool for single-cell transposable element locus-level analysis of scRNA sequencing (Stellarscope) that reassigns multimapped reads to specific genomic loci using an expectation maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define cell subsets not identified by standar"],"journal":["Cell reports methods"],"pagination":["101086"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12296447"],"repository":["biostudies-literature"],"pubmed_title":["A single-cell transposable element atlas of human cell identity."],"pmcid":["PMC12296447"],"pubmed_authors":["Greenig M","O'Mara MM","Lawrence E","Ostrowski MA","Reyes-Gopar H","Hernandez-Lemus E","Randall KN","Singh B","Dopkins N","Powell TR","Fei T","Duarte RRR","Nixon DF","Iniguez LP","Lin J","Marston JL","Sandoval-Motta S","Bendall ML"],"additional_accession":[]},"is_claimable":false,"name":"A single-cell transposable element atlas of human cell identity.","description":"Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex biological systems. However, most sequencing studies overlook the contribution of transposable element (TE) expression to the transcriptome. The quantification of locus-specific TE expression in scRNA-seq experiments is challenging due to their repetitive sequence content and poorly characterized annotations. Here, we developed a computational tool for single-cell transposable element locus-level analysis of scRNA sequencing (Stellarscope) that reassigns multimapped reads to specific genomic loci using an expectation maximization algorithm. Using Stellarscope, we built an atlas of TE expression in human PBMCs. We found that locus-specific TEs delineate cell types and define cell subsets not identified by standar","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Jul","modification":"2026-07-15T14:24:39.166Z","creation":"2025-08-28T03:08:44.719Z"},"accession":"S-EPMC12296447","cross_references":{"pubmed":["40543500"],"doi":["10.1016/j.crmeth.2025.101086"]}}