Figure 2
ABX464 has no global effect on cellular splicing. (A) The effect of ABX464 on infected and uninfected CD4+ T cells was tested by a high-throughput RNAseq approach. Sixteen libraries were constructed using 4 conditions: uninfected (DMSO_NI), uninfected treated with ABX464 (ABX464_NI), infected (DMSO_I) and infected treated with ABX464 (464_I), corresponding to 4 donors. Approximately 38 million reads (more than 50% of the total raw reads) were aligned to exons of the human genome sequence in each of the samples. (B) Multidimensional scaling analysis (MDS) was used to interpret major trends in the data. (C) Alternative splicing (AS) events of cellular genes were classified into five major groups (left panel): Alternative 5′ splice site (A5SS, orange), Alternative 3′ splice site (A3SS, blue), Skipped exon (SE, gray), Mutually exclusive exons (MXE, gray) and Retained exon (RI, yellow). AS event counts comparing infected vs uninfected samples (DMSO_I vs DMSO_NI), uninfected vs uninfected treated by ABX464 (DMSO_NI vs 464_NI), infected vs infected treated by ABX464 (DMSO_I vs 464_I) and after 50% depletion CBC in IPS (IPS depletion of CBC by 50%) (right panel). (D) By comparing exon coverage reads of a common highly expressed gene (B2M) between the ABX464 and DMSO conditions in the 4 donors, we confirmed that ABX464 did not increase splicing events in B2M. (E) Volcano plot of DMSO_I vs DMSO_NI (upper panel), DMSO_NI vs 464_NI (middle panel), DMSO_I vs 464_I (lower panel). The gene expression variation generated by ABX464 treatment was very low in infected (6 downregulated genes) and uninfected (6 downregulated genes) samples.
