Extended Data Fig. 3: Gene modules that align near peak viremia and are differentially expressed in pDCs are enriched for response to interferon.

a, Enrichment of modules from P1 in Fig. 2b against the IPA Interferon Signaling canonical pathway; FDR corrected Right-Tailed Fisher’s Exact Test. See Supplementary Table 4 for gene lists and their sizes. b, Heatmap of median expression of genes upregulated in PBMCs from SIV infection of rhesus macaques (n=8) compared to day 0 (fold change > 2) in Bosinger et al.²¹ depicted independently for each cell type in P1. Only genes differentially expressed across all time points by ANOVA in a given cell type are shown. c, Differential expression results for IRF7 in each cell type (except plasmablasts and mDCs which do not have enough cells to test, n < 4) between cells from 2 weeks and pre-infection + 1 year; implemented using the “bimod” likelihood ratio test in Seurat⁴⁴. See Supplementary Table 2 for cell numbers per cell type per timepoint. d, Representative gating scheme for single-cell pDC sorts. n = 8 samples. e, Heatmap of genes differentially expressed between pDCs captured at the same timepoints as peak interferon responses and 1-year post HIV infection. Two-sided Wilcoxon rank sum test; number of cells per timepoint: Peak – 159; 1-Year – 184. f, Same as a for the modules in Fig. 2d for P2, P3, and P4. See Supplementary Table 2 for cell numbers per cell type per timepoint. g, Mean gene expression (log scaled) of MX1 and CXCL10 over time in each individual separated by cell type. Shaded area denotes 95% confidence interval of the mean. h, Scoring of pDCs in each participant using a core interferon signature specific to that participant. Number of cells per participant and time point: P1 Peak – 31; P1 1-Year – 79; P2 Peak – 48; P2 1-Year – 20; P3 Peak – 42; P3 1-Year – 28; P4 Peak – 16; P4 1-Year – 57. i, Heatmap of gene frequency across interferon response GMs in each participant.