Extended Data Fig. 2: Validity of HIV DNA⁺ cell transcriptome sequencing after FIND-seq.

(a) HIV DNA⁺ J-Lat T cells and HIV DNA⁻ Raji B cells were mixed at a 1:100 ratio and then subjected to FIND-seq and whole transcriptome sequencing. In parallel, extracted RNA samples from J-Lat cells and Raji cells were subjected to standard RNA-seq processing for comparison. (b) Droplet cytometry plot representing sorting of HIV DNA⁺ cells from the J-Lat:Raji mixture. (c) Correlation of gene expression differences between HIV DNA⁺ cells and HIV DNA⁻ cells (determined after FIND-seq) with gene expression differences between J-Lat cells and Raji cells (determined after standard RNA-seq). Points are coloured according to concordance of statistical significance in differential gene expression (DGE) results between FIND-seq and standard RNA-seq. Purple denotes genes significantly different (p < 0.05) in both FIND-seq and standard RNA-seq; grey denotes genes not significantly different in either FIND-seq or standard RNA-seq; blue denotes genes with discordant significance between standard and FIND-seq samples. Pearson’s R and p values were calculated in R v4.1.0. (d) Volcano plot of genes that were differentially expressed between HIV DNA⁺ and HIV DNA⁻ cells after FIND-seq, coloured by expected direction of change. Blue: differentially expressed genes found in gene set GSE10325 (M3077: CD4 T cell vs B cell down), red: differentially expressed genes found in GSE10325 (M3076: CD4 T cell vs B cell up). (e) Gene set enrichment pre-ranked analysis (GSEA) comparing transcriptomic differences between HIV DNA⁺ and HIV DNA⁻ cell samples sequenced from the J-Lat:Raji mixture after FIND-seq to previously reported differences between CD4 T cells and B cells (CD4 TCELL VS BCELL UP, M3076; CD4 TCELL VS BCELL DN, M3077).