Cell type-specific immune phenotypes predict loss of insulin secretion in new-onset type 1 diabetes

Peripheral blood samples were collected from control-arm subjects enrolled in 6 clinical trials conducted by the Immune Tolerance Network and Type 1 Diabetes TrialNet. The included trials evaluated immune-modifying therapy in new-onset T1D, with similar trial timecourses, primary outcomes, and data and sample collection. Total RNA was isolated from whole blood samples and then globin-reduced. RNAseq libraries were prepared from the globin-reduced RNA. Subjects from the control arms of 6 clinical trials in new-onset T1D were aggregated to evaluate variation in disease course in the immediate post-diagnostic period. All trials used serum C-peptide concentration after a mixed-meal tolerance test as the primary outcome, with an initial trial duration of approximately two years, with longer-term follow-up in some cases. We obtained RNA-seq data from all available subject visits (N = 138 subjects), ranging from the time of study entry to three years, for a total of 496 samples (mean 3.6 samples per subject). Three samples were removed due to SNP-based kinship values indicating sample contamination or mis-identification; these samples are excluded from the submitted dataset. Of the remaining 493 samples, 471 yielded high-quality RNA-seq data from unique visits consistent with subject annotation, and were used in downstream analyses.