ScRNAseq analysis of data from patients with T1D and healthy donors

Datasets for the analysis of scRNAseq data for the manuscript: Imbalance of stem-like and effector T cell states in children with early type 1 diabetes across conventional and regulatory subsets Veronika Niederlova1,2, Ales Neuwirth1, Vit Neuman3, Juraj Michalik1, Bela Charvatova1, Martin Modrak4, Zdenek Sumnik3, Ondrej Stepanek1 1 Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia2 Department of Cell Biology, Faculty of Science, Charles University in Prague, Czechia3 Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague & Motol University Hospital, Prague, Czechia4 Department of Bioinformatics, Second Faculty of Medicine, Charles University, Prague, Czechia Please see the associated GitHub repository for recapitulation of the analysis: https://github.com/Lab-of-Adaptive-Immunity/dia. The repository contains four folders: the folder initdata contains rds files from different batches, with only basic QC and no integration; the folder processed_v2 contains integrated datasets as they appear in the manuscript. If you have questions re: metadata, annotation, or if you would like to get the .rds files from conventional CD4 and CD8 (without unconventional T cells and NK cells), just let us know, we're always happy to help. We weren't able to upload these because of the file size limits; the folder data_from_other_studies contains raw and/or processed data from published studies which we used to validate our findings; the folder flow_data contains data from our flow cytometry analysis.