SCINA- and Astir- but not AnnoSpat-predicted beta cells from T1D samples, where beta cells are rare, showed high levels of immune cell-restricted proteins CD57 and HLA-ABC (Fig. 2a–c, rows 2, 5, and 6; Supplementary Fig. 1a–c, rows 1, 4, and 5). Here, B3GAT1 is linked to type 1 diabetes mellitus.