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[Preprint]. 2023 Dec 12:2023.11.17.567619. Originally published 2023 Nov 18. [Version 2] doi: 10.1101/2023.11.17.567619

Figure 7. Effect of HIV-1 transduction and of IFIH1 knockdown on the dendritic cell transcriptome.

Figure 7.

CD14+ monocytes from three blood donors (coded M27, M28, and M29) were transduced with shRNA-puromycin resistance vectors targeting either IFIH1 or Luc control, as indicated. Cells were selected with puromycin for three days, and differentiated into dendritic cells. A, Immunoblot shows steady-state levels of IFIH1 protein for the indicated samples. Then, dendritic cells were either transduced with HIV-1-GFP or left untransduced. At 48 hrs, RNA was isolated from cells and poly(A)-selected libraries were generated for RNA-Seq. Volcano plot depicting differentially expressed genes after HIV-1 challenge in Luc knockdown (KD) control cells (B), or in IFIH1 KD cells (C), as determined by RNA-Seq (log2[fold change of normalized counts]>1; P<0.01, determined by DESeq2), for the indicated samples. D, Reactome pathway analysis based on 276 differentially expressed genes in HIV-1 transduced Luc-KD cells in comparison to HIV-1 transduced IFIH1-KD cells. Gene Ontology-produced P values (as determined by Fisher’s exact test) with FDR correction (Benjamini-Hochberg method) are shown.