CD4+ T cells transduced with either pTRIP-SFFV-GFP or pTRIP-SFFV-GFP-RELA or pTRIP-SFFV-GFP-RELA K5R and RNA was isolated 4 d after transduction. The analysis was performed by GenoSplice. Analysis of sequencing data quality, reads repartition (e.g., for potential ribosomal contamination), inner distance size estimation, genebody coverage, and strand-specificity of the library were performed using FastQC v0.11.2, Picard-Tools v1.119, Samtools v1.0, and RSeQC v2.3.9. Reads were mapped using STAR v2.7.5a on the human hg38 genome assembly and read count was performed using featureCount from SubRead v1.5.0. Gene expression was estimated as described previously (Paillet et al., 2021 (link)) using Human FAST DB v2022_1 annotations. Only genes expressed in at least one of the two compared conditions were analyzed further. Genes were considered as expressed if their FPKM value was greater than the FPKM of 96% of the intergenic regions (background). Analysis at the gene level was performed using DESeq2 using experiment ID in the DESeq2 GLM model. Genes were considered differentially expressed for fold changes ≥1.5 and P values ≤0.05. Pathway analyses were performed using WebGestalt v0.4.4 merging results from upregulated and downregulated genes only, as well as all regulated genes. Pathways and networks were considered significant with P values ≤0.05. The results of this analysis were compared to those from Zhao et al. (2015) (link) corresponding to the GSE68329 GEO dataset ID. Regulated genes from Zhao et al. (2015) (link) were retrieved using GEO2R using adjusted P value ≤0.05 and fold change ≥ 1.5. Gene expression data have been deposited at GEO (accession no. GSE182647).