HIV latency transcriptomics of resting CD4+ T cells

I met with Walter to get a update on the status of this project. After some delay last year in the lab he is now expecting to have the sequencing data in March this year. NB: for now this is bulk RNAseq on single cell as initially stated.

The experiment consists of FACS sorting of a) primary CD4 T-cells (from patients) and b) the Jarket CD4 T-cell line that have been infected with HIV. Two reporter genes are used to separate cells by FACS into three subsets: HIV-negative, HIV-latent and HIV-active. In addition the HIV-latent population were activated, again applying FACS sorting. The question Walter wants to answer is what differentiates latently-infected cells from cells that are actively infected (i.e. virions replicating) in terms of human gene expression in these cells.

Out existing RNAseq pipeline should be sufficient to process the expected Illumina MiSeq data however R scripts will have to be developed for downstream differential abundance testing.