Extension of the dataset shown in Fig. 2e, wild-type (n = 5 mice) and TOX∆ (n = 5 mice) P14 T cells were transferred into C57BL/6 hosts and infected with LCMV clone 13 or Armstrong. Cells were isolated 8 or 20 days later and analysed by next-generation sequencing. a, Volcano plots comparing wild-type and TOX∆ P14 T cells isolated from hosts infected with clone 13 after 8 or 20 days, lines indicate filter criteria of log 2 ± 1 and adjusted P = 0.05; genes upregulated in wild-type (orange) or ∆TOX (green) are highlighted and numbers above the thresholds are indicated. b, z-scores (DESeq2 package) depicting heat maps are a supervised selection of molecules. Wald statistics and Benjamini and Hochberg corrections were used for data analysis. c, Venn diagrams showing the overlap between three DEG lists defined by filtering the data shown in Extended Data Fig. 1a (dysfunctional versus normal T cells; red) and Extended Data Fig. 1b (re-expanded dysfunctional versus re-expanded memory T cells; blue) for average expression >6, P < 0.05 and |log 2 (WT/TOX∆)| ≥ 0.3 and the dataset shown in a, b for mean expression >50, P < 0.05 and |log 2 (WT/TOX∆)| ≥ 0.3. Numbers depict the DEG overlap between the datasets. d, The datasets from a and Extended Data Fig. 1a were filtered as indicated in c and loaded into the IPA software (Qiagen). Build-in algorithms (core analysis) were used to identify regulators that are linked to these datasets. Note that these analyses were performed independently for both datasets. Yet, there was a >60% overlap among the top-50 ranked regulators that were identified for both datasets (data not shown). The graph shows the regulators that are shared between both datasets and depicts the P values that are assigned to the regulator in the two datasets (x axis data are linked to Extended Data Fig. 1a, y axis data are linked to a and Fig. 2e). Highlighted in colour are regulators with P ≤ 10−8 in both datasets. e, The number of genes that are linked to the regulator identified for the dataset shown in Extended Data Fig. 1a (dysfunctional versus normal T cells) and the fraction of the linked genes that are differentially expressed in ∆TOX T cells. f, The Venn diagram is derived from c and compares only the datasets shown in a, Extended Data Fig. 1a and Fig. 2e. The 269 overlapping DEGs were imported into IPA and a core analysis was performed. Plots show the P values for the associated upstream transcription factors or transcription regulators (jointly referred to as TR) plus the number of genes linked to these molecules. g, Day 8 LCMV Armstrong gene expression profiles as explained for a and b.