ScRNAseq analysis of data from patients with T1D and healthy donors
Peripheral blood mononuclear cells (PBMCs) were collected from children newly diagnosed with type 1 diabetes (T1D) and from healthy donors. A subset of the same T1D patients was re-sampled one year after diagnosis to assess longitudinal changes. CD4 and CD8 T cells were sorted and subjected to single-cell RNA sequencing using the 10x Genomics Chromium platform (5' v2 chemistry). Libraries were prepared according to the manufacturer's protocol and sequenced on an Illumina NovaSeq 6000 instrument. Raw sequencing data were processed with Cell Ranger (10x Genomics) for demultiplexing, alignment to the GRCh38 reference genome, and UMI counting. Downstream analyses, including clustering, differential gene expression, and gene set enrichment, were performed using Seurat and custom R scripts.