Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8+ T-cell epitopes. Gfeller et al

Supplementary Tables. Table S1: List of HLA-I peptidomics samples considered in this work, related to Figure 1. Table S2: List of HLA-I ligands used to train MixMHCpred2.2, related to Figure 2. Table S3: List of peptides including both HLA-I ligands (i.e., positives) and random peptides (i.e., negatives) used to benchmark MixMHCpred2.2, related to Figure 2. The HLA-I ligands in the first ten datasets come from Gfeller et al. The HLA-I ligands in the last eleven datasets come from Pyke et al. Table S4: List of immunogenic and non-immunogenic peptides used to train PRIME2.0, related to Figure 3. Table S5: Information about SARS-CoV-2 peptides and donor samples used in T-cell assays, related to Figure 4. (A) List of 213 peptides from the SARS-CoV-2 proteome included in the peptide pool. (B) List of the 15 most common HLA-I alleles used to make predictions. (C) Information about the six donors used to screen SARS-CoV-2 peptides for immunogenicity. Table S6: List of TCR sequences and UMI counts (alpha and beta chains) obtained from CD8+ T cells recognizing seven SARS-CoV-2 epitopes, related to Figure 4.补充表格。 表S1：本研究纳入的人类白细胞抗原I类（HLA-I）肽组学样本列表，对应图1。 表S2：用于训练MixMHCpred2.2的人类白细胞抗原I类配体列表，对应图2。 表S3：用于基准测试MixMHCpred2.2的肽段列表，其中既包含人类白细胞抗原I类配体（即阳性样本）也包含随机肽段（即阴性样本），对应图2。前十组数据集内的人类白细胞抗原I类配体来源于Gfeller等人的研究，后十一组数据集内的人类白细胞抗原I类配体来源于Pyke等人的研究。 表S4：用于训练PRIME2.0的免疫原性与非免疫原性肽段列表，对应图3。 表S5：用于T细胞实验的严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）肽段及供体样本信息，对应图4。(A) 肽段库中包含的213条严重急性呼吸综合征冠状病毒2型蛋白质组肽段列表；(B) 用于生成预测的15种最常见人类白细胞抗原I类等位基因列表；(C) 用于筛选严重急性呼吸综合征冠状病毒2型肽段免疫原性的6名受试供体的相关信息。 表S6：从识别7种严重急性呼吸综合征冠状病毒2型表位的CD8阳性T细胞（CD8+ T细胞）中获取的T细胞受体（TCR）序列及唯一分子标识符（UMI）计数（α链与β链）列表，对应图4。