Seurat R objects for Březina et al: Claudin 1–mediated positioning of DC1 to mTECs is essential for maintenance of central tolerance. J Exp Med 2 March 2026

Submitted files contain processed and annotated single-cell RNA-Seq data for publication Claudin 1–mediated positioning of DC1 to mTECs is essential for maintenance of central tolerance by Jiří Březina et. al published in the Journal of Experimental Medicine (see related works). Files are R objects of class "Seurat" exported as RDS format, use readRDS() function for loading. Data were processed from 10x cellranger filtered matrices using Seurat v4, for specific parameters see @commands slot of the objects. Annotated cell type is described in "Cell_Type" column in the cell metadata, objects contain raw+normalized counts, reductions and projections. The raw sequencing data are available in the BioStudies database under the accession number E-MTAB-14319 (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-14319). Detailed description: Brezina_etal_26_Seurat_Figure_S1B_all_cells.rds: Merged TdTOMATO+ and TdTOMATO- cells (not integrated), this object contains all the cells in the dataset and is underlying figure S1-B in the publication. Brezina_etal_26_Seurat_Figure_1B_DCs_Mono_Mac.RDS: Merged TdTOMATO+ and TdTOMATO- cells. This object is a subset containing only clusters annotated as DCs, monocytes and macrophages. Seurat integration was first used to integrate data from TdTOMATO+ and TdTOMATO- datasets before subsetting. The integrated assay is included with reductions and projections calculated based on this assay. This object is the founding data for figure 1-B in the publication.