Extended Data Fig. 1: Assessing the MHCII peptidomes of the pancreatic islets, pancreatic lymph nodes and spleens from NOD mice.

a, Representative FACS plots showing the APC populations in the islets from 8-10-week old female NOD mice. The major APCs in the islet were the islet macrophages (CD45⁺CD11c⁺F4/80⁺) and dendritic cells (CD45⁺CD11c⁺F4/80^–), along with a minor population of B cells (CD45⁺CD11c^–F4/80^–B220⁺). Data are representative of n = 4 independent experiment including n = 6 mice per experiment. b, Workflow for isolating the MHCII peptidome followed by mass spectrometry and immunological analyses. c, The lengths of all the peptides identified in the MHCII peptidomes from the indicated sites. Most of the peptides were 14-17 residues long, and a small number was longer than 25 residues. Data (mean) are from the mass spectrometry analysis of the MHCII peptidomes depicted in Supplementary Tables 1–3. d, Antigen presentation assay showing responses of an Ins1C-specific CD4⁺ T cell hybridoma to C3g7 APCs treated with or without chloroquine and pulsed with the full-length 29-residue Ins1C:33-61. The assay measures IL-2 production by the CD4⁺ T cell hybridoma during stimulation with the cognate antigen, assessed by the proliferation (³H incorporation) of the IL-2-depedent cell line CTLL-2 (see Methods). The Data (mean ± s.e.m.) are representative of n = 2 independent experiments with similar results.