HIV-CRISPR screen of HIV-1 CA-P90A and CA-N74D mutant viruses with the PIKAHIV library

Illumina sequencing data used in HIV-CRISPR screen with an ISG-specific sgRNA library (PIKAHIV) to find genes that block infection by the N74D and P90A HIV-1 capsid mutant viruses in THP-1 monocytic cells. For more information on the library and approach see Ohainle et al. eLife 2018 (PMID: 30520725). All screens performed here were done in a clonal ZAP-KO cell line (ZAP may inhibit the HIV-CRISPR vector used in the screen). Here we screen the Cyclophilin A-binding deficient mutant P90A and the CPSF6-binding deficient mutant N74D together with a wild type HIV-1 virus. The N74D screen was performed both with IFN treatment and without. These two HIV-1 capsid mutant viruses are hypersensitive to the effects of IFN. Overall design: An HIV-CRISPR screen targeting Interferon-Stimulated Genes in which enrichment of 20bp sgRNA sequences is compared in viral RNA to the library representation of the sgRNA sequences in genomic DNA. 2 biological replicates were performed in ZAP Knockout THP-1 clonal cell lines for all screens, except the HIV-1 CA-P90A mutant screen with IFN and the HIV-1 CA-N74D mutant screen without IFN in which only a single replicate for the viral RNA was performed. Cells were infected following treatment overnight with IFN and viral supernatants and cell pellets collected 3 days post-infection. sgRNA representation in viral RNA is compared to genomic DNA to determine which sgRNAs are over- or under-represented in the viral population.