Extended Data Fig. 3 |. Supporting analyses for HHV-6 reactivation using Serratus.

(a) Comparison of read number matching to any of the annotated 16 T-cell libraries from Serratus for HHV-6A or HHV-6B. A distinct library is compared for HHV-6A and HHV-6B, connected by a line, quantification from Serratus. Libraries are sorted by HHV-6B expression, which was higher for all libraries than HHV-6A. (b) Heatmap of HHV-6B transcripts across the four samples with highest RNA expression in libraries from Serratus. Shown are the first 40 genes (based on genomic coordinate order) from the HHV-6B transcriptome and the number of reads that pseudoalign to each transcript. (c) Summary of % RNA molecules aligning to the HHV-6B reference in the naive CD4+ culture from the LaMere et al. dataset; compare to Fig. 1e. (d) Summary of HHV-6-SNV analysis and overlap across the two RNA-seq samples with highest HHV-6 reactivation (from Fig. 1d,e) (e) Summary of HHV-6B expression in a previously reported ATAC-seq atlas²⁵, showing sorted T cells from Patient 59, an individual with CTCL, who had detectable levels of HHV-6B DNA within cells. (f) Smoothed coverage (rolling mean of 500 base pairs) over the four libraries from Patient 59, showing the coverage across the HHV-6B reference genome. (g) Schematic and results of previously described²⁶ adoptive Treg therapy culture showing HHV-6 reactivation after reanalysis of primary data.